diff --git a/tools/bash/runfiles/runfiles.bash b/tools/bash/runfiles/runfiles.bash
index d3aa0c3d238d14..d0aedd41deca89 100644
--- a/tools/bash/runfiles/runfiles.bash
+++ b/tools/bash/runfiles/runfiles.bash
@@ -122,16 +122,51 @@ function rlocation() {
         echo >&2 "INFO[runfiles.bash]: rlocation($1): looking in RUNFILES_MANIFEST_FILE ($RUNFILES_MANIFEST_FILE)"
       fi
       local -r result=$(grep -m1 "^$1 " "${RUNFILES_MANIFEST_FILE}" | cut -d ' ' -f 2-)
-      if [[ -e "${result:-/dev/null}" ]]; then
-        if [[ "${RUNFILES_LIB_DEBUG:-}" == 1 ]]; then
-          echo >&2 "INFO[runfiles.bash]: rlocation($1): found in manifest as ($result)"
-        fi
-        echo "$result"
-      else
+      if [[ -z "$result" ]]; then
+        # If path references a runfile that lies under a directory that itself
+        # is a runfile, then only the directory is listed in the manifest. Look
+        # up all prefixes of path in the manifest and append the relative path
+        # from the prefix if there is a match.
+        local prefix="$1"
+        local prefix_result=
+        local new_prefix=
+        while true; do
+          new_prefix="${prefix%/*}"
+          [[ "$new_prefix" == "$prefix" ]] && break
+          prefix="$new_prefix"
+          prefix_result=$(grep -m1 "^$prefix " "${RUNFILES_MANIFEST_FILE}" | cut -d ' ' -f 2-)
+          [[ -z "$prefix_result" ]] && continue
+          local -r candidate="${prefix_result}${1#"${prefix}"}"
+          if [[ -e "$candidate" ]]; then
+            if [[ "${RUNFILES_LIB_DEBUG:-}" == 1 ]]; then
+              echo >&2 "INFO[runfiles.bash]: rlocation($1): found in manifest as ($candidate) via prefix ($prefix)"
+            fi
+            echo "$candidate"
+            return 0
+          fi
+          # At this point, the manifest lookup of prefix has been successful,
+          # but the file at the relative path given by the suffix does not
+          # exist. We do not continue the lookup with a shorter prefix for two
+          # reasons:
+          # 1. Manifests generated by Bazel never contain a path that is a
+          #    prefix of another path.
+          # 2. Runfiles libraries for other languages do not check for file
+          #    existence and would have returned the non-existent path. It seems
+          #    better to return no path rather than a potentially different,
+          #    non-empty path.
+          break
+        done
         if [[ "${RUNFILES_LIB_DEBUG:-}" == 1 ]]; then
           echo >&2 "INFO[runfiles.bash]: rlocation($1): not found in manifest"
         fi
         echo ""
+      else
+        if [[ -e "$result" ]]; then
+          if [[ "${RUNFILES_LIB_DEBUG:-}" == 1 ]]; then
+            echo >&2 "INFO[runfiles.bash]: rlocation($1): found in manifest as ($result)"
+          fi
+          echo "$result"
+        fi
       fi
     else
       if [[ "${RUNFILES_LIB_DEBUG:-}" == 1 ]]; then
diff --git a/tools/bash/runfiles/runfiles_test.bash b/tools/bash/runfiles/runfiles_test.bash
index e2b514910a6599..e532824770fa3c 100755
--- a/tools/bash/runfiles/runfiles_test.bash
+++ b/tools/bash/runfiles/runfiles_test.bash
@@ -139,10 +139,14 @@ function test_init_manifest_based_runfiles() {
 a/b $tmpdir/c/d
 e/f $tmpdir/g h
 y $tmpdir/y
+c/dir $tmpdir/dir
 EOF
   mkdir "${tmpdir}/c"
   mkdir "${tmpdir}/y"
+  mkdir -p "${tmpdir}/dir/deeply/nested"
   touch "${tmpdir}/c/d" "${tmpdir}/g h"
+  touch "${tmpdir}/dir/file"
+  touch "${tmpdir}/dir/deeply/nested/file"
 
   export RUNFILES_DIR=
   export RUNFILES_MANIFEST_FILE=$tmpdir/foo.runfiles_manifest
@@ -153,10 +157,18 @@ EOF
   [[ "$(rlocation a/b)" == "$tmpdir/c/d" ]] || fail
   [[ "$(rlocation e/f)" == "$tmpdir/g h" ]] || fail
   [[ "$(rlocation y)" == "$tmpdir/y" ]] || fail
-  rm -r "$tmpdir/c/d" "$tmpdir/g h" "$tmpdir/y"
+  [[ "$(rlocation c)" == "" ]] || fail
+  [[ "$(rlocation c/di)" == "" ]] || fail
+  [[ "$(rlocation c/dir)" == "$tmpdir/dir" ]] || fail
+  [[ "$(rlocation c/dir/file)" == "$tmpdir/dir/file" ]] || fail
+  [[ "$(rlocation c/dir/deeply/nested/file)" == "$tmpdir/dir/deeply/nested/file" ]] || fail
+  rm -r "$tmpdir/c/d" "$tmpdir/g h" "$tmpdir/y" "$tmpdir/dir"
   [[ -z "$(rlocation a/b)" ]] || fail
   [[ -z "$(rlocation e/f)" ]] || fail
   [[ -z "$(rlocation y)" ]] || fail
+  [[ -z "$(rlocation c/dir)" ]] || fail
+  [[ -z "$(rlocation c/dir/file)" ]] || fail
+  [[ -z "$(rlocation c/dir/deeply/nested/file)" ]] || fail
 }
 
 function test_manifest_based_envvars() {
diff --git a/tools/cpp/runfiles/runfiles_src.cc b/tools/cpp/runfiles/runfiles_src.cc
index 75d606d7c080ad..2d3078065b5f78 100644
--- a/tools/cpp/runfiles/runfiles_src.cc
+++ b/tools/cpp/runfiles/runfiles_src.cc
@@ -25,6 +25,7 @@
 #include <unistd.h>
 #endif  // _WIN32
 
+#include <algorithm>
 #include <fstream>
 #include <functional>
 #include <map>
@@ -176,9 +177,24 @@ string Runfiles::Rlocation(const string& path) const {
   if (IsAbsolute(path)) {
     return path;
   }
-  const auto value = runfiles_map_.find(path);
-  if (value != runfiles_map_.end()) {
-    return value->second;
+  const auto exact_match = runfiles_map_.find(path);
+  if (exact_match != runfiles_map_.end()) {
+    return exact_match->second;
+  }
+  if (!runfiles_map_.empty()) {
+    // If path references a runfile that lies under a directory that itself is a
+    // runfile, then only the directory is listed in the manifest. Look up all
+    // prefixes of path in the manifest and append the relative path from the
+    // prefix to the looked up path.
+    std::size_t prefix_end = path.size();
+    while ((prefix_end = path.find_last_of('/', prefix_end - 1)) !=
+           string::npos) {
+      const string prefix = path.substr(0, prefix_end);
+      const auto prefix_match = runfiles_map_.find(prefix);
+      if (prefix_match != runfiles_map_.end()) {
+        return prefix_match->second + "/" + path.substr(prefix_end + 1);
+      }
+    }
   }
   if (!directory_.empty()) {
     return directory_ + "/" + path;
diff --git a/tools/cpp/runfiles/runfiles_test.cc b/tools/cpp/runfiles/runfiles_test.cc
index 67a9048d9df5a7..cbe2952c1904cd 100644
--- a/tools/cpp/runfiles/runfiles_test.cc
+++ b/tools/cpp/runfiles/runfiles_test.cc
@@ -252,6 +252,8 @@ TEST_F(RunfilesTest, ManifestBasedRunfilesRlocationAndEnvVars) {
   EXPECT_EQ(r->Rlocation("/Foo"), "/Foo");
   EXPECT_EQ(r->Rlocation("c:/Foo"), "c:/Foo");
   EXPECT_EQ(r->Rlocation("c:\\Foo"), "c:\\Foo");
+  EXPECT_EQ(r->Rlocation("a/b/file"), "c/d/file");
+  EXPECT_EQ(r->Rlocation("a/b/deeply/nested/file"), "c/d/deeply/nested/file");
 }
 
 TEST_F(RunfilesTest, DirectoryBasedRunfilesRlocationAndEnvVars) {
@@ -316,6 +318,8 @@ TEST_F(RunfilesTest, ManifestAndDirectoryBasedRunfilesRlocationAndEnvVars) {
   EXPECT_EQ(r->Rlocation("/Foo"), "/Foo");
   EXPECT_EQ(r->Rlocation("c:/Foo"), "c:/Foo");
   EXPECT_EQ(r->Rlocation("c:\\Foo"), "c:\\Foo");
+  EXPECT_EQ(r->Rlocation("a/b/file"), "c/d/file");
+  EXPECT_EQ(r->Rlocation("a/b/deeply/nested/file"), "c/d/deeply/nested/file");
   AssertEnvvars(*r, mf->Path(), dir);
 }
 
diff --git a/tools/java/runfiles/Runfiles.java b/tools/java/runfiles/Runfiles.java
index 0dd90cce437858..9a3aa26c4517a9 100644
--- a/tools/java/runfiles/Runfiles.java
+++ b/tools/java/runfiles/Runfiles.java
@@ -227,7 +227,21 @@ private static String findRunfilesDir(String manifest) {
 
     @Override
     public String rlocationChecked(String path) {
-      return runfiles.get(path);
+      String exactMatch = runfiles.get(path);
+      if (exactMatch != null) {
+        return exactMatch;
+      }
+      // If path references a runfile that lies under a directory that itself is a runfile, then
+      // only the directory is listed in the manifest. Look up all prefixes of path in the manifest
+      // and append the relative path from the prefix if there is a match.
+      int prefixEnd = path.length();
+      while ((prefixEnd = path.lastIndexOf('/', prefixEnd - 1)) != -1) {
+        String prefixMatch = runfiles.get(path.substring(0, prefixEnd));
+        if (prefixMatch != null) {
+          return prefixMatch + '/' + path.substring(prefixEnd + 1);
+        }
+      }
+      return null;
     }
 
     @Override
diff --git a/tools/java/runfiles/testing/RunfilesTest.java b/tools/java/runfiles/testing/RunfilesTest.java
index 92f303b2c5e8b6..e98ca554a8a27d 100644
--- a/tools/java/runfiles/testing/RunfilesTest.java
+++ b/tools/java/runfiles/testing/RunfilesTest.java
@@ -249,10 +249,15 @@ public void testManifestBasedRlocation() throws Exception {
         new MockFile(
             ImmutableList.of(
                 "Foo/runfile1 C:/Actual Path\\runfile1",
-                "Foo/Bar/runfile2 D:\\the path\\run file 2.txt"))) {
+                "Foo/Bar/runfile2 D:\\the path\\run file 2.txt",
+                "Foo/Bar/Dir E:\\Actual Path\\Directory"))) {
       Runfiles r = Runfiles.createManifestBasedForTesting(mf.path.toString());
       assertThat(r.rlocation("Foo/runfile1")).isEqualTo("C:/Actual Path\\runfile1");
       assertThat(r.rlocation("Foo/Bar/runfile2")).isEqualTo("D:\\the path\\run file 2.txt");
+      assertThat(r.rlocation("Foo/Bar/Dir")).isEqualTo("E:\\Actual Path\\Directory");
+      assertThat(r.rlocation("Foo/Bar/Dir/File")).isEqualTo("E:\\Actual Path\\Directory/File");
+      assertThat(r.rlocation("Foo/Bar/Dir/Deeply/Nested/File"))
+          .isEqualTo("E:\\Actual Path\\Directory/Deeply/Nested/File");
       assertThat(r.rlocation("unknown")).isNull();
     }
   }
diff --git a/tools/python/runfiles/runfiles.py b/tools/python/runfiles/runfiles.py
index 3a597cbb36a92b..03cff1c27ee386 100644
--- a/tools/python/runfiles/runfiles.py
+++ b/tools/python/runfiles/runfiles.py
@@ -174,7 +174,22 @@ def __init__(self, path):
     self._runfiles = _ManifestBased._LoadRunfiles(path)
 
   def RlocationChecked(self, path):
-    return self._runfiles.get(path)
+    """Returns the runtime path of a runfile."""
+    exact_match = self._runfiles.get(path)
+    if exact_match:
+      return exact_match
+    # If path references a runfile that lies under a directory that itself is a
+    # runfile, then only the directory is listed in the manifest. Look up all
+    # prefixes of path in the manifest and append the relative path from the
+    # prefix to the looked up path.
+    prefix_end = len(path)
+    while True:
+      prefix_end = path.rfind("/", 0, prefix_end - 1)
+      if prefix_end == -1:
+        return None
+      prefix_match = self._runfiles.get(path[0:prefix_end])
+      if prefix_match:
+        return prefix_match + "/" + path[prefix_end + 1:]
 
   @staticmethod
   def _LoadRunfiles(path):
diff --git a/tools/python/runfiles/runfiles_test.py b/tools/python/runfiles/runfiles_test.py
index 1212bbaad83340..70168cbb6107e5 100644
--- a/tools/python/runfiles/runfiles_test.py
+++ b/tools/python/runfiles/runfiles_test.py
@@ -28,26 +28,26 @@ def testRlocationArgumentValidation(self):
     self.assertRaises(ValueError, lambda: r.Rlocation(None))
     self.assertRaises(ValueError, lambda: r.Rlocation(""))
     self.assertRaises(TypeError, lambda: r.Rlocation(1))
-    self.assertRaisesRegexp(ValueError, "is not normalized",
-                            lambda: r.Rlocation("../foo"))
-    self.assertRaisesRegexp(ValueError, "is not normalized",
-                            lambda: r.Rlocation("foo/.."))
-    self.assertRaisesRegexp(ValueError, "is not normalized",
-                            lambda: r.Rlocation("foo/../bar"))
-    self.assertRaisesRegexp(ValueError, "is not normalized",
-                            lambda: r.Rlocation("./foo"))
-    self.assertRaisesRegexp(ValueError, "is not normalized",
-                            lambda: r.Rlocation("foo/."))
-    self.assertRaisesRegexp(ValueError, "is not normalized",
-                            lambda: r.Rlocation("foo/./bar"))
-    self.assertRaisesRegexp(ValueError, "is not normalized",
-                            lambda: r.Rlocation("//foobar"))
-    self.assertRaisesRegexp(ValueError, "is not normalized",
-                            lambda: r.Rlocation("foo//"))
-    self.assertRaisesRegexp(ValueError, "is not normalized",
-                            lambda: r.Rlocation("foo//bar"))
-    self.assertRaisesRegexp(ValueError, "is absolute without a drive letter",
-                            lambda: r.Rlocation("\\foo"))
+    self.assertRaisesRegex(ValueError, "is not normalized",
+                           lambda: r.Rlocation("../foo"))
+    self.assertRaisesRegex(ValueError, "is not normalized",
+                           lambda: r.Rlocation("foo/.."))
+    self.assertRaisesRegex(ValueError, "is not normalized",
+                           lambda: r.Rlocation("foo/../bar"))
+    self.assertRaisesRegex(ValueError, "is not normalized",
+                           lambda: r.Rlocation("./foo"))
+    self.assertRaisesRegex(ValueError, "is not normalized",
+                           lambda: r.Rlocation("foo/."))
+    self.assertRaisesRegex(ValueError, "is not normalized",
+                           lambda: r.Rlocation("foo/./bar"))
+    self.assertRaisesRegex(ValueError, "is not normalized",
+                           lambda: r.Rlocation("//foobar"))
+    self.assertRaisesRegex(ValueError, "is not normalized",
+                           lambda: r.Rlocation("foo//"))
+    self.assertRaisesRegex(ValueError, "is not normalized",
+                           lambda: r.Rlocation("foo//bar"))
+    self.assertRaisesRegex(ValueError, "is absolute without a drive letter",
+                           lambda: r.Rlocation("\\foo"))
 
   def testCreatesManifestBasedRunfiles(self):
     with _MockFile(contents=["a/b c/d"]) as mf:
@@ -122,7 +122,7 @@ def testFailsToCreateManifestBasedBecauseManifestDoesNotExist(self):
     def _Run():
       runfiles.Create({"RUNFILES_MANIFEST_FILE": "non-existing path"})
 
-    self.assertRaisesRegexp(IOError, "non-existing path", _Run)
+    self.assertRaisesRegex(IOError, "non-existing path", _Run)
 
   def testFailsToCreateAnyRunfilesBecauseEnvvarsAreNotDefined(self):
     with _MockFile(contents=["a b"]) as mf:
@@ -140,14 +140,22 @@ def testFailsToCreateAnyRunfilesBecauseEnvvarsAreNotDefined(self):
 
   def testManifestBasedRlocation(self):
     with _MockFile(contents=[
-        "Foo/runfile1", "Foo/runfile2 C:/Actual Path\\runfile2",
-        "Foo/Bar/runfile3 D:\\the path\\run file 3.txt"
+        "Foo/runfile1",
+        "Foo/runfile2 C:/Actual Path\\runfile2",
+        "Foo/Bar/runfile3 D:\\the path\\run file 3.txt",
+        "Foo/Bar/Dir E:\\Actual Path\\Directory",
     ]) as mf:
       r = runfiles.CreateManifestBased(mf.Path())
       self.assertEqual(r.Rlocation("Foo/runfile1"), "Foo/runfile1")
       self.assertEqual(r.Rlocation("Foo/runfile2"), "C:/Actual Path\\runfile2")
       self.assertEqual(
           r.Rlocation("Foo/Bar/runfile3"), "D:\\the path\\run file 3.txt")
+      self.assertEqual(
+          r.Rlocation("Foo/Bar/Dir/runfile4"),
+          "E:\\Actual Path\\Directory/runfile4")
+      self.assertEqual(
+          r.Rlocation("Foo/Bar/Dir/Deeply/Nested/runfile4"),
+          "E:\\Actual Path\\Directory/Deeply/Nested/runfile4")
       self.assertIsNone(r.Rlocation("unknown"))
       if RunfilesTest.IsWindows():
         self.assertEqual(r.Rlocation("c:/foo"), "c:/foo")