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LIP: 0031
Title: Introduce Merkle trees and inclusion proofs
Author: Alessandro Ricottone <>
Status: Active
Type: Informational
Created: 2020-02-19
Updated: 2021-12-01
Requires: 0027


The purpose of this LIP is to define a generic Merkle Tree structure and a format for proof-of-inclusion that can be used in different parts of the Lisk protocol.


This LIP is licensed under the Creative Commons Zero 1.0 Universal.


A Merkle tree is an authenticated data structure organized as a tree (Fig. 1). The hash of each data block is stored in a node on the base layer, or leaf, and every internal node of the tree, or branch, contains a cryptographic hash that is computed from the hashes of its two child nodes. The top node of the tree, the Merkle root, uniquely identifies the data array from which the tree was constructed.

Merkle trees allow for an efficient proof-of-inclusion, where a Prover shows to a Verifier that a certain data block is part of the authenticated data array by sending them a proof with an audit path. The audit path contains the node hashes necessary to recalculate the Merkle root, without requiring the Verifier to store or the Prover to reveal the whole data array. For an array of size N, the audit path contains at most Log(N) hashes, and the proof-of-inclusion is verified by calculating at most Log(N) hashes (here and later Log indicates the base 2 logarithm of the argument). Furthermore, if the Verifier wants to check the presence of multiple data blocks at once, it is possible to obtain some hashes directly from the data blocks and reuse them for multiple simultaneous verifications.

In Bitcoin, the transactions contained in a block are stored in a Merkle tree. This allows for Simplified Payment Verification (SPV), i.e., a lightweight client can verify that a certain transaction is included in a block without having to download the whole block or Bitcoin blockchain.

In Ethereum, the roots of Merkle Patricia trees are included in each block header to authenticate the global state of the blockchain (stateRoot), the transactions within the block (transactionsRoot and receiptsRoot) and the smart contract data (storageRoot for each Ethereum account).

The inclusion of Merkle trees can be beneficial in several parts of the Lisk protocol:

  • Storing the root of a Merkle tree for the transactions in the payloadHash in the block header would allow users to verify efficiently that a transaction has been included in the block. At the moment the payloadHash contains the hash of the serialized transactions, and to verify the presence of a single transaction users have to download the whole block. After the proposed change to limit the block size to 15kb, a full block will contain approximately 120 transactions at most. In this case, performing a proof-of-inclusion will require to query 7 hashes, and the size of the corresponding proof would be 232 bytes (see "Proof serialization" section below). Thus, the amount of data to be queried to verify the presence of a single transaction in a full block is reduced by ~98%.
  • Merkle trees as an authenticated data structure can be helpful to create a snapshot of the account states as well as the transaction and block history, for example for the "Introduce decentralized re-genesis" roadmap objective.


This LIP defines the general specifications to build a Merkle tree from a data array, calculate the Merkle root and perform a proof-of-inclusion in the Lisk protocol. We require the following features:

  • Cryptographically secure: the data array can not be altered without changing the Merkle root.
  • Proof-of-inclusion: presence of data blocks in the data array or in the tree can be verified without querying the whole tree.
  • Efficient append: new data blocks can be appended to the data array, and the tree is updated with at most Log(N) operations for an array of size N.

We consider two possible implementations for a Merkle tree: regular Merkle trees (RMT) and sparse Merkle trees (SMT).

Regular Merkle Trees

In a RMT, data blocks are inserted in the tree in the order in which they appear in the data array. Hence, the order can not be altered to reproduce the same Merkle root consistently. This also implies that in a RMT it is not possible to insert a new leaf in an arbitrary position efficiently, as this changes the position in the tree of many other leaf nodes, so that the number of branch nodes to be updated is proportional to the size of the tree N. On the other hand, RMTs are suitable for append-only data array, as appending a new elements to the array updates a number of branch nodes proportional to Log(N) only.

RMT accepting input data blocks with arbitrary length are susceptible to second pre-image attacks. In a second pre-image attack, the goal of the attacker is to find a second input x′ that hashes to the same value of another given input x, i.e. find x’ ≠ x such that hash(x) = hash(x’). In Merkle trees, this corresponds to having two different input data arrays x and x’ with the same Merkle root. This is trivial in an RMT: choose x = [D1, D2, D3, D4] and x’ = [D1, D2, hash(D3) || hash(D4)], where || indicates input concatenation. To solve this problem we use a different hashing function for leaf and branch nodes [1].

RMTs are in general easier to implement because of their limited storage requirements. Furthermore, the data array can be sorted in such a way that most queries would ask for a proof-of-inclusion for data blocks stored consecutively, allowing then for smaller audit paths. For example this is the case for the Merkle tree built out of blocks headers where blocks are stored according to their height, and a typical query could ask to verify the presence of consecutive blocks in the blockchain.

Sparse Merkle Trees

In a SMT, all possible leaf nodes are initialized to the empty value. Every leaf occupies a fixed position, indexed by its key. In a SMT, the order of insertion of the data blocks is not relevant, as all leaf nodes are indexed by their respective keys.

In a SMT it is possible to obtain a proof-of-absence for a certain key by simply showing that the empty value is stored in the corresponding leaf with a proof-of-inclusion. SMTs are easy to update: once a leaf node with a certain key is updated, one has to update only Log(N) branch nodes up the tree. For 256 bits-long keys, there are 2256 possible leaf nodes, and the height of the tree is 256. Hence, each update changes the value of 256 nodes.

SMT are too large to be stored explicitly and require further optimization to reduce their size. For example, one could decide to place a leaf node at the highest subtree with only 1 non-null entry and trim out all empty nodes below it. This is the approach taken by the Aergo State trie.

We choose to implement RMTs and reserve the possibility to implement SMTs in different parts of the Lisk protocols in the future.

Proof-of-Inclusion Protocol

In this section, we clarify the steps necessary for a proof-of-inclusion and introduce some useful terminology. The elements constituting a proof-of-inclusion are:

  1. merkleRoot: The Merkle root of the tree built from the data array data.
  2. queryHashes: An array of bytes. The elements of the array can be the hash values of either leaf or branch nodes.
  3. proof: The proof itself, consisting of 3 parts: size, idxs and siblingHashes:
  4. size: The total number of data blocks in the data array (the length of data).
  5. idxs: An array of indices corresponding to the position in the tree of the nodes corresponding to queryHashes.
  6. siblingHashes: The hashes that are part of the audit path, an array of bytes necessary to compute the Merkle root starting from queryHashes.

The procedure for a proof-of-inclusion is as follows:

  1. Verifier: The Verifier knows merkleRoot and sends the Prover an array of hash values queryHashes for which they wish to obtain a proof-of-inclusion.
  2. Prover:
  3. The Prover finds the nodes corresponding to queryHashes in the Merkle tree and generates the array of corresponding indices idxs.
  4. The Prover generates siblingHashes and transmits the complete proof to the Verifier; proof contains size, idxs and siblingHashes.
  5. Verifier: The Verifier uses proof to recalculate the Merkle root using elements from queryHashes and checks that it equals merkleRoot.

In Fig. 1 we sketch a simple proof-of-inclusion for data block data1. The Verifier asks the Prover for a proof for queryHashes=[leafHash(data1)]. The Prover sends back proof with size=5, idxs=[0001]and siblingHashes=[h0, h6, h4].


Merkle tree with path

Figure 1: A Merkle tree built from the data array [data0, ...data4]. Here N=5. The leaf hash HL=leafHash of the data blocks (grey rectangles) is inserted as leaf node (green rectangles). Branch nodes (brown rectangles) contain the branch hash HB=branchHash of two children nodes below them. Unpaired nodes are just passed up the tree until a pairing node is found. The siblingHashes for data1 (red-bordered rectangles) includes h0, h6 and h4 in this order. The layers of the tree, starting from the bottom, have 5, 2, 1 and 1 nodes.

In this section we define the general construction rules of a Merkle tree. Furthermore, we specify how the Merkle root of a data array is calculated and how the proof construction and verification work. The protocol to efficiently append a new element to the tree is specified in Appendix B.

We assume data blocks forming the data array are bytes of arbitrary length, and the hash values stored in the tree and the Merkle root are bytes of length 32. We define the leaf- and branch-nodes hash function by prepending a different constant flag to the data before hashing [1, Section 2.1. “Merkle Hash Trees“]:

  • leafHash(msg) = hash(LEAF_PREFIX || msg)
  • branchHash(msg) = hash(BRANCH_PREFIX || msg)

where || indicates bytes concatenation and LEAF_PREFIX and BRANCH_PREFIX are two constants set to:

  • LEAF_PREFIX = 0x00
  • BRANCH_PREFIX = 0x01

Here the function hash returns the SHA-256 hash of the input. Data blocks from the data array are hashed and inserted in the tree as leaf nodes. Then nodes are hashed together recursively in pairs until the final Merkle root is reached. If N is not a power of two, some layers will have an odd number of nodes, resulting in some nodes being unpaired during the construction of the tree. In this case we just pass the node to the level above without hashing it (Fig. 1 where N=5).

Merkle Root

For an input data array of arbitrary length of the form:

  • data: An (ordered) array of bytes of arbitrary length,

we define a unique bytes value of length 32, the Merkle root merkleRoot.

The Merkle root is calculated recursively by splitting the input data into two arrays, one containing the first k data blocks and one for the rest, where k is the largest power of 2 smaller than N, until the leaf nodes are reached and their leafHash is returned [1]. Notice that the order of the input array matters to reproduce the same Merkle root.

function merkleRoot(data):
  size = data.length
  if size == 0: return EMPTY_HASH
  if size == 1: return leafHash(data[0])
  k = largestPowerOfTwoSmallerThan(size)
  // Split the data array into 2 subtrees. leftTree from index 0 to index k (not included), rightTree for the rest
  leftTree = data[0:k]
  rightTree = data[k:size]
  return branchHash(merkleRoot(leftTree) || merkleRoot(rightTree))

The Merkle root of an empty data array is equal to the hash of an empty string: EMPTY_HASH=SHA-256("").


Merkle tree with indices

Figure 2: An indexed Merkle tree. The binary index uniquely identifies the position of each node in the tree: the length of the index, together with the tree height, specifies the layer the node belongs to, while the index specifies the position within the layer.

For an input data array of arbitrary length of the form:

  • queryHashes: an array of bytes of length 32,

we define an array proof containing 3 parts:

  1. size: The total length of the data array data.
  2. idxs: An array indicating the position in the data array data of the elements to be verified, corresponding to queryHashes.
  3. siblingHashes: An array of bytes, containing the node values necessary to recompute the Merkle root starting from queryHashes.

Proof Construction

The Prover searches for the position in the tree of each node corresponding to the values given in queryHashes, and generates the corresponding array idxs assigning an index to the node according to the following rules:

  • If the node is not part of the tree, it is assigned a special index (see "Proof serialization" section), and the node is not taken into consideration when constructing the rest of the proof.
  • The index of a node present in the tree equals its position in the layer converted to binary, with a fixed length equal to the tree height minus the layer number, with 0s prepended as necessary (see Fig. 2). Notice that in this representation each index starts with a 0, and the layer the node belongs to can be inferred from the length of the index and size.

Notice that the elements of idxs are placed in the same order as the corresponding values in queryHashes and not sorted. The Prover generates siblingHashes by adding the necessary hashes in a bottom-up/left-to-right order. For the example in Fig.1, starting from the base layer and the leftmost node, the hash values added in the audit path are h0, h6 and h4. This order reflects the order in which siblingHashes is consumed by the Verifier during the verification.

Proof Serialization

The proof is serialized according to the specifications defined in LIP 0027 "A generic, deterministic and size efficient serialization method" using the following JSON schema:

proof = {
  "type": "object",
  "properties": {
    "size": {
      "dataType": "uint64",
      "fieldNumber": 1
    "idxs": {
      "type": "array",
      "items": {
        "dataType": "uint64"
      "fieldNumber": 2
    "siblingHashes": {
      "type": "array",
      "items": {
        "dataType": "bytes"
      "fieldNumber": 3
  "required": [

In particular:

  • size is encoded as a uint64.
  • Each index in idxs is prepended a 1 and is encoded as a uint64. The extra 1 is added as a delimiter to set the correct index length. At the moment of decoding, each index is converted from unsigned integer to binary, the first bit (which equals 1) is dropped and only the following bits are kept. Furthermore, we use the special index 0 to flag any element which is not part of the data array, and as such can be discarded during the verification. Notice that this does not constitute a proof-of-absence for that element.
  • The elements of siblingHashes are encoded as an array of bytes of length 32.

The hex-encoded proof for the example in Fig. 1 is proof=0x0805||0x120111||0x1a20||h0||0x1a20||h6||0x1a20||h4, with a length L=107 bytes.


The Verifier obtains size from the proof, and calculates the structure of the tree from size. In particular, they know how many nodes are present in each layer with the following simple rule:

  • There are a total number of layers equal to height=ceiling(Log(size))+1.
  • The base layer contains a number of nodes equal to size.
  • Each other layer contains half the number of nodes of the layer below. If this is an odd number, we round either down and up, alternating every time it is necessary and starting by rounding down.

For example, to size=13 corresponds height=5 and #nodesPerLayer=[13, 6, 3, 2, 1].

With the structure of the tree and idxs, the Verifier is able to identify the position in the tree of each element of queryHashes and to drop all elements that are not part of the tree using the special flag. They consume siblingHashes in the same order in which it was constructed to calculate the Merkle root. Finally, they check that the resulting Merkle root equals merkleRoot to complete the verification.

Backwards Compatibility

This proposal does not introduce any forks in the network, as it only defines the specification to build a Merkle tree in the Lisk protocol. Future protocol changes involving the introduction of Merkle trees (such as LIP 0032 "Replace payloadHash with Merkle tree root in block header" or the "Introduce decentralized re-genesis" roadmap objective) will require this proposal.

Reference Implementation

  1. Mitsuaki Uchimoto: LiskHQ/lisk-sdk#5467
  2. Shusetsu Toda: LiskHQ/lisk-sdk#5342

Appendix A: Proof-of-Inclusion Implementation

We describe two functions to perform a proof-of-inclusion:

  1. generateProof(queryHashes): This function generates and returns the inclusion proof for the input hash values queryHashes.
  2. verify(queryHashes, proof, merkleRoot): This function checks that the inclusion proof proof is valid for the input hash values queryHashes with respect to the Merkle root merkleRoot, returning a boolean value.

We split generateProof into 3 different subroutines and define the following 3 accessory function, one for each part of the proof (see section "Proof-of-inclusion"):

function getSize():
  return length of the underlying data array
function getIndices(queryHashes):
  idxs = []
  for elem in queryHashes:
    currentNode = tree node with node.hash == elem
    if currentNode not in tree:
      idx = constant value to flag missing nodes
      idx = binary(currentNode.index), with length = height - currentNode.layer
    push idx to idxs
  return idxs
function getSiblingHashes(idxs):
  siblingHashes = []
  for idx in idxs:
    if idx == missing node flag:
      remove idx from idxs
    currentNode = tree node with node.index == idx

    if currentNode is unpaired:
      sibling = sibling node of currentNode
      // Notice that the sibling node could come from a lower layer
      if sibling.index in idxs:
        remove sibling.index from idxs
        push sibling.hash to siblingHashes

    remove idx from idxs
    // Parent index is idx without last bit
    parentIndex = idx >> 1
    push parentIndex to idxs
  return siblingHashes

generateProof is then simply given by:

function generateProof(queryHashes):
  size = getSize()
  idxs = getIndices(queryHashes)
  siblingHashes = getSiblingHashes(idxs)
  return proof = [size, idxs, siblingHashes]

We define the accessory function calculatePathNodes. This function calculates all nodes of the tree that can be obtained from the elements of queryHashes, and returns them as a dictionary. calculatePathNodes works similarly to generateProof, but gets missing nodes from siblingHashes instead of adding them to it.

function calculatePathNodes(queryHashes, size, idxs, siblingHashes):
  // tree is a dictionary where we store the known values
  tree = {}
  for (idx, hash) in zip(idxs, queryHashes):
    if idx == missing node flag:
      remove idx from idxs
    tree[idx] = node with node.hash == hash

  for idx in idxs:
    node = tree[idx]
    // Notice that the sibling node could come from a lower layer
    siblingIndex = index of sibling of node
    // Parent index is idx without last bit
    parentIndex = idx >> 1
    if node is unpaired:
      if siblingIndex in tree:
        siblingHash = tree[siblingIndex].hash
        siblingHash = siblingHashes[0]
        siblingHashes = siblingHashes[1:]
      if node.side == left:
        tree[parentIndex] = parentNode
                            with parentNode.hash = branchHash(node.hash || siblingHash)
        tree[parentIndex] = parentNode
                            with parentNode.hash = branchHash(siblingHash || node.hash)
    remove idx from idxs
    push parentIndex to idxs

  return tree

verify just checks that the root node returned by calculatePathNodes as hash value equal to merkleRoot.

function verify(queryHashes, proof, merkleRoot):
  [size, idxs, siblingHashes] = proof
  calculatedTree = calculatePathNodes(queryHashes, size, idxs, siblingHashes)
  // The root node has index 0
  calculatedRoot = calculatedTree["0"]
  return calculatedRoot == merkleRoot

Appendix B: Append-Path Implementation

Merkle tree with update path

Figure 4: Some examples of append paths for Merkle trees of size 2 to 6. On the left of each tree, the binary representation of their respective size is indicated, top to bottom. Whenever a 1 is present, a node in the layer is part of the append path, which therefore contains at most a number of elements equal to Log(N).

Adding new data blocks to the tree updates the value of at most Log(N) branch nodes. We define the append path to be an array of bytes containing the branch-node values necessary to compute the updated tree (Fig. 4). Adding new data blocks updates the append path as well. Assigning a digit of the binary representation of N to each layer of the tree, starting from the bottom, we notice that a layer contains a node which is part of the append path if and only if we assigned 1 to it. Therefore, the append path contains at most Log(N) elements, and updating the tree requires to calculate at most Log(N) hashes.

To append a new element we need to do the following:

  1. Add the leaf hash of the element to the base layer.
  2. Update the affected branch nodes in the tree.
  3. Update the append path.

In some circumstances, one can be interested in checking that a new data block has been appended correctly to the tree. This can be done without storing the whole tree by recomputing the new Merkle root. In this case it is sufficient to store and update the data array length, the append path and the Merkle root.

In the following pseudocode, the function append takes as input the new data block newElement and updates the Merkle tree. The strategy is to use the binary representation of size: each digit di ∈ {0, 1} labels a layer of the tree according to the power of 2 it represents, starting with the rightmost digit d0 for the base layer (Fig. 4). Possibly the root has no digit assigned to it (in this case we can assign it a 0).

function append(newElement):
  // 1. Add the leaf hash of the element to the base layer
  hash = leafHash(newElement)
  add new node to base layer, with node.hash = hash
  // 2. Update the affected branch nodes in the tree
  height = current height of the tree
  size = length of the underlaying data array
  for j in range(height):
    // d is the l-th binary digit of size (from the right)
    d = (size >> j) & 1
    if d == 1:
      hash = branchHash(appendPath[k] || hash)
      if k == 0: add new node to layer above, with node.hash = hash
      else: set node.hash = hash, where node is the rightmost node in the layer above
  // 3. Update the append path
  for j in range(height):
    // d is the h-th binary digit of size (from the right)
    d = (size >> j) & 1
    if d == 0:
    // Split appendPath into bottomPath = appendPath[:l] (bottom layers) and topPath = appendPath[l:] (upper layers)
  bottomPath = appendPath[:j]
  topPath = appendPath[j:]
  // Hash the new element recursively with the hashes in bottomPath
  for h in bottomPath:
    hash = branchHash(h || hash)
  // The new append path contains the final hash concatenated with topPath
  newAppendPath = [hash] + topPath

Appendix C: Proof-of-Inclusion Protocol for Leaf Nodes

In this section, we define a protocol that can be used for verifying that a set of data blocks queryData is part of the tree. The procedure is similar to the one for a proof-of-inclusion, but before generating the proof and running the verification, the array queryData is converted to the array containing the corresponding leaf hash values queryHashes.

In analogy with a normal proof-of-inclusion, we describe two functions to perform a proof-of-inclusion for an array of data blocks:

  1. generateDataBlockProof(queryData): This function returns the inclusion proof for an input array of data blocks queryData.
  2. verifyDataBlock(queryData, proof, merkleRoot): This function checks that the data blocks in queryData are stored in the tree using the inclusion proof proof and comparing the calculated tree root to the root of the tree merkleRoot.
function generateDataProof(queryData):
  queryHashes = [leafHash(data) for data in queryData]
  proof = generateProof(queryHashes)
  return proof
function verifyDataBlock(queryData, proof, merkleRoot):
  queryHashes = [leafHash(data) for data in queryData]
  check = verify(queryHashes, proof, merkleRoot)
  return check

Appendix D: Right Witness Implementation

Given a Merkle tree of size N, it is possible to compute the Merkle root starting from a partial version of the tree, i.e. the root and append path of the tree after idx<=N data blocks had been appended to the tree, and a right witness. Similarly to the append path, the right witness is an array of hash values that can be consumed and hashed together to calculate the root. The difference is that, while elements of the append path are always hashed on the left, elements of the right witness are always hashed on the right. In particular, to calculate the root of the complete tree, one only needs the append path and right witness of the partial tree.

We define the function generateRightWitness(idx). This function generates the right witness of the partial tree of size idx. The input is an integer idx between 0 and the current size of the tree and the returned value an array of hashes.

function generateRightWitness(idx):
  if idx == 0:
    return tree.appendPath
  if idx == tree.size:
    return []

  rightWitness = []
  // incrementalIdx is initially equal to idx and it is later increased to signal that a subtree has been completed
  incrementalIdx = idx
  lastLeftNodeIndex = idx - 1

  for l in range(tree.height):
    // d is the l-th binary digit of incrementalIdx (from the right)
    d = (incrementalIdx >> l) & 1
    if d == 1:
      currentNode = tree node with node.index == lastLeftNodeIndex >> l

      if currentNode is unpaired:
      // We want to push the sibling node hash only if it is located "on the right" of current node in the tree
      sibling = sibling node of currentNode
      if sibling.layer > currentNode.layer or sibling.index < currentNode.index:

      push sibling.hash to rightWitness
      // Complete the subtree after right hashing
      incrementalIdx += (1 << l)

  return rightWitness

We define the accessory functions calculateRootFromPath(path) and calculateRootFromRightWitness(idx, appendPath, rightWitness).

The function calculateRootFromPath(path) calculates the root by iteratively hashing elements of path.

function calculateRootFromPath(path):
  if path.length == 0:
    return EMPTY_HASH
  currentHash = path[0]
  path = path[1:]

  while path.length > 0:
    pathHash = path[0]
    path = path[1:]
    currentHash = branchHash(pathHash || currentHash)

  return currentHash

The function calculateRootFromRightWitness calculates and returns the Merkle root of the complete tree from the append path at index idx and the right witness obtained from generateRightWitness(idx). The inputs are an integer idx, the append path appendPath and right witness rightWitness at index idx (explained above).

function calculateRootFromRightWitness(idx, appendPath, rightWitness):
  if appendPath.length == 0:
    return calculateRootFromPath(rightWitness)
  if rightWitness.length == 0:
    return calculateRootFromPath(appendPath)
  l = 0
  // incrementalIdx is initially equal to idx and it is later increased to signal that a subtree has been completed
  incrementalIdx = idx
  while appendPath.length > 0 or rightWitness.length > 0:
    // d is the l-th binary digit of idx (from the right)
    d = (idx >> l) & 1
    if appendPath.length > 0 and d == 1:
      if currentHash is not initialized:
        leftHash = appendPath[0]
        appendPath = appendPath[1:]
        rightHash = rightWitness[0]
        rightWitness = rightWitness[1:]
        currentHash = branchHash(leftHash || rightHash)
        incrementalIdx += (1 << l)
        leftHash = appendPath[0]
        appendPath = appendPath[1:]
        currentHash = branchHash(leftHash || currentHash)

    // r is the l-th binary digit of incrementalIdx (from the right)
    r = (incrementalIdx >> l) & 1
    if rightWitness.length > 0 and r == 1:
      rightHash = rightWitness[0]
      rightWitness = rightWitness[1:]
      currentHash = branchHash(currentHash || rightHash)
      incrementalIdx += (1 << l)


  return currentHash

The function verifyRightWitness(idx, appendPath, rightWitness, merkleRoot) checks that the Merkle root computed using calculateRootFromRightWitness(idx, appendPath, rightWitness) equals the Merkle root of the tree merkleRoot. The returned value is a boolean, indicating the success of the check.

function verifyRightWitness(idx, appendPath, rightWitness, merkleRoot):
  calculatedRoot = calculateRootFromRightWitness(idx, appendPath, rightWitness)
  return calculatedRoot == merkleRoot

Appendix E: Update of Leaf Nodes

The value of leaf nodes can be updated efficiently with a protocol similar to the one for the verification of the inclusion proof. This time the calculated intermediary hashes are also stored, updating the branch nodes in the path, and the new Merkle root is returned.

The function update(idxs, updateData) updates the leaf nodes corresponding to idxs and the branch nodes in the path. The input is an array of integers idxs and an array of bytes values updateData. The function returns the new Merkle root of the tree.

function update(idxs, updateData):
  updateHashes = [leafHash(data) for data in updateData]
  size = getSize()
  siblingHashes = getSiblingHashes(idxs)
  calculatedTree = calculatePathNodes(updateHashes, size, idxs, siblingHashes)
  store elements of calculatedTree
  // The root node has index 0
  calculatedRoot = calculatedTree["0"]
  return calculatedRoot

The root of the tree can also be updated in a trustless setup, using the inclusion proof for the leaf nodes that would be changed. In this case, the proof is first checked using the old value of the leaf nodes oldData against the current Merkle root merkleRoot by calling verifyDataBlock(oldData, proof, merkleRoot). Afterwards, the new Merkle root can be calculated using the calculateRootFromUpdateData(updateData, proof) function. This function is very similar to update, but does not store the updated values. The input is an array of bytes values updateData and an inclusion proof proof for these values. The function returns the new Merkle root of the tree.

function calculateRootFromUpdateData(updateData, proof):
  updateHashes = [leafHash(data) for data in updateData]
  [size, idxs, siblingHashes] = proof
  calculatedTree = calculatePathNodes(updateHashes, size, idxs, siblingHashes)
  // The root node has index 0
  calculatedRoot = calculatedTree["0"]
  return calculatedRoot

Appendix F: Merkle Aggregation

Merkle trees can support efficient and verifiable queries of specific content through Merkle aggregation [2]. In a Merkle aggregation, extra information is stored on each node of the Merkle tree as a flag. When a new leaf is appended to the tree, its flag is included in the hash, for example by prepending it to the leaf node value, and is stored together with the resulting hash in a tuple leafNodeValue=(flag, hash(flag || LEAF_PREFIX || message)). A parent node combines the flags from its children nodes (performing the OR operation on the flags) and stores them: branchNodeValue=(flag, hash(flag || BRANCH_PREFIX || childrenHashes)).

The Verifier can then query the Merkle tree for all those elements containing a given flag. The Prover constructs a pruned Merkle tree, where each subtree not containing any flagged node is removed and only the highest node in the pruned subtree is appended to the result. The Verifier can check that each pruning has been done correctly by asking for an inclusion proof for a leaf node in that pruned subtree. They can then verify that the leaf node did not contain the flag. Therefore, the Verifier receives a list of flagged elements with a proof that no element is missing from the list (no false positives).

If we want to allow for F different flags, each node will store an F-bits array. Each flag is set by setting the corresponding bit to 1, and branch nodes apply bitwise or on the children-nodes flags.

Appendix G: Example of Proof-of-Inclusion Protocol for Transaction IDs

As an example, the following procedure can be used to verify the presence of a set of transactions in a block.


  1. Choose a set of transaction IDs queryIDs and a block ID blockID. We assume the client already knows merkleRoot, the Merkle root of the transactions included in the respective block.
  2. Ask the server (for example a full node) for the proof necessary to verify the transactions corresponding to queryIDs, for example with a get request passing (queryIDs, blockID) as parameters.


  1. Get block from blockID. If blockID does not give a valid block, return an empty proof.
  2. Get the list of transactions blockTxs from the block payload.
  3. Compute the queryHashes array by hashing every element in queryIDs with the leafHash function.
  4. Get the indices idxs of the requested queryHashes. If a transaction is not in the block, set its index to a flag indicating that it is not part of the block.
  5. Generate siblingHashes.
  6. Transmit proof=[blockTxs.length, idxs, siblingHashes].


  1. Compute the queryHashes array by hashing every element in queryIDs with the leafHash function.
  2. Reorder queryHashes based on the order in which the indices in idxs are given. If a transaction has been flagged, drop the corresponding hash value from queryHashes. Notice that this does not constitute a proof-of-non-inclusion for the transaction.
  3. Verify the presence of the transactions calling verify(queryHashes, proof, merkleRoot).


[1] Laurie, B., Langley, A. and Kasper, E., 2014. Certificate Transparency. ACM Queue, 12(8), pp.10-19.

[2] Crosby, S.A. and Wallach, D.S., 2009, August. Efficient Data Structures For Tamper-Evident Logging. In USENIX Security Symposium (pp. 317-334).