diff --git a/c/tests/test_tables.c b/c/tests/test_tables.c
index 9ac80f86fe..c2d310d2b5 100644
--- a/c/tests/test_tables.c
+++ b/c/tests/test_tables.c
@@ -4087,6 +4087,48 @@ test_sort_tables_mutation_times(void)
     tsk_treeseq_free(&ts);
 }
 
+static void
+test_sort_tables_canonical_errors(void)
+{
+    int ret;
+    tsk_table_collection_t tables;
+    ret = tsk_table_collection_init(&tables, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+    tables.sequence_length = 1;
+
+    ret = tsk_node_table_add_row(&tables.nodes, 0, 0.0, TSK_NULL, TSK_NULL, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+    ret = tsk_site_table_add_row(&tables.sites, 0.0, "x", 1, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+    ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 2, 0.0, "a", 1, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+    ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 3, 0.0, "b", 1, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+    ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 1, 0.0, "c", 1, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+    ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 2, 0.0, "d", 1, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+
+    ret = tsk_table_collection_canonicalise(&tables, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MUTATION_PARENT_INCONSISTENT);
+
+    ret = tsk_mutation_table_clear(&tables.mutations);
+    CU_ASSERT_FATAL(ret >= 0);
+    ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 2, 0.0, "a", 1, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+    ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 3, 0.0, "b", 1, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+    ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 1, 0.0, "c", 1, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+    ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, -1, 0.0, "d", 1, NULL, 0);
+    CU_ASSERT_FATAL(ret >= 0);
+
+    ret = tsk_table_collection_canonicalise(&tables, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+
+    tsk_table_collection_free(&tables);
+}
+
 static void
 test_sort_tables_canonical(void)
 {
@@ -6028,6 +6070,7 @@ main(int argc, char **argv)
         { "test_edge_update_invalidates_index", test_edge_update_invalidates_index },
         { "test_copy_table_collection", test_copy_table_collection },
         { "test_sort_tables_errors", test_sort_tables_errors },
+        { "test_sort_tables_canonical_errors", test_sort_tables_canonical_errors },
         { "test_sort_tables_canonical", test_sort_tables_canonical },
         { "test_sorter_interface", test_sorter_interface },
         { "test_dump_unindexed", test_dump_unindexed },
diff --git a/c/tskit/core.c b/c/tskit/core.c
index 42ea25e37a..7c5dc57da8 100644
--- a/c/tskit/core.c
+++ b/c/tskit/core.c
@@ -281,6 +281,9 @@ tsk_strerror_internal(int err)
         case TSK_ERR_MUTATION_PARENT_AFTER_CHILD:
             ret = "Parent mutation ID must be < current ID";
             break;
+        case TSK_ERR_MUTATION_PARENT_INCONSISTENT:
+            ret = "Mutation parent references form a loop.";
+            break;
         case TSK_ERR_INCONSISTENT_MUTATIONS:
             ret = "Inconsistent mutations: state already equal to derived state";
             break;
diff --git a/c/tskit/core.h b/c/tskit/core.h
index da11798303..eba37ddc24 100644
--- a/c/tskit/core.h
+++ b/c/tskit/core.h
@@ -246,7 +246,8 @@ not found in the file.
 #define TSK_ERR_MUTATION_PARENT_DIFFERENT_SITE                      -500
 #define TSK_ERR_MUTATION_PARENT_EQUAL                               -501
 #define TSK_ERR_MUTATION_PARENT_AFTER_CHILD                         -502
-#define TSK_ERR_INCONSISTENT_MUTATIONS                              -503
+#define TSK_ERR_MUTATION_PARENT_INCONSISTENT                        -503
+#define TSK_ERR_INCONSISTENT_MUTATIONS                              -504
 #define TSK_ERR_UNSORTED_MUTATIONS                                  -505
 #define TSK_ERR_NON_SINGLE_CHAR_MUTATION                            -506
 #define TSK_ERR_MUTATION_TIME_YOUNGER_THAN_NODE                     -507
diff --git a/c/tskit/tables.c b/c/tskit/tables.c
index d79a46d726..b9558e21bb 100644
--- a/c/tskit/tables.c
+++ b/c/tskit/tables.c
@@ -4905,6 +4905,10 @@ tsk_table_sorter_sort_mutations_canonical(tsk_table_sorter_t *self)
         p = mutations->parent[j];
         while (p != TSK_NULL) {
             sorted_mutations[p].num_descendants += 1;
+            if (sorted_mutations[p].num_descendants > (int) num_mutations) {
+                ret = TSK_ERR_MUTATION_PARENT_INCONSISTENT;
+                goto out;
+            }
             p = mutations->parent[p];
         }
     }