diff --git a/c/CHANGELOG.rst b/c/CHANGELOG.rst
index e75b9e2bf1..70ead6e4ea 100644
--- a/c/CHANGELOG.rst
+++ b/c/CHANGELOG.rst
@@ -10,6 +10,11 @@ In development
 - Update to kastore 2.1.3 to include file security fix (:user:`jeromekelleher`,
   :pr:`3478`).
 
+- Fix ``tsk_table_collection_link_ancestors`` accepting a sample or ancestor ID
+  equal to the number of nodes, which indexed node-sized arrays one past their
+  end. Such IDs now return ``TSK_ERR_NODE_OUT_OF_BOUNDS``.
+  (:user:`asystemoffields`, :issue:`3484`, :pr:`3492`)
+
 --------------------
 [1.3.1] - 2026-03-06
 --------------------
diff --git a/c/tests/test_tables.c b/c/tests/test_tables.c
index 7fca96563a..013c1d3eb1 100644
--- a/c/tests/test_tables.c
+++ b/c/tests/test_tables.c
@@ -7625,6 +7625,19 @@ test_link_ancestors_input_errors(void)
         &tables, samples, 2, ancestors, 2, 0, &result);
     CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);
 
+    /* Sample and ancestor IDs one past the last node */
+    ancestors[0] = 4;
+    samples[0] = (tsk_id_t) tables.nodes.num_rows;
+    ret = tsk_table_collection_link_ancestors(
+        &tables, samples, 2, ancestors, 2, 0, &result);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);
+
+    samples[0] = 0;
+    ancestors[0] = (tsk_id_t) tables.nodes.num_rows;
+    ret = tsk_table_collection_link_ancestors(
+        &tables, samples, 2, ancestors, 2, 0, &result);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);
+
     /* Duplicate sample IDs */
     ancestors[0] = 4;
     samples[0] = 1;
diff --git a/c/tskit/tables.c b/c/tskit/tables.c
index d673619141..c6db8e17a0 100644
--- a/c/tskit/tables.c
+++ b/c/tskit/tables.c
@@ -7905,7 +7905,7 @@ ancestor_mapper_init_samples(ancestor_mapper_t *self, tsk_id_t *samples)
 
     /* Go through the samples to check for errors. */
     for (j = 0; j < self->num_samples; j++) {
-        if (samples[j] < 0 || samples[j] > (tsk_id_t) self->tables->nodes.num_rows) {
+        if (samples[j] < 0 || samples[j] >= (tsk_id_t) self->tables->nodes.num_rows) {
             ret = tsk_trace_error(TSK_ERR_NODE_OUT_OF_BOUNDS);
             goto out;
         }
@@ -7932,7 +7932,8 @@ ancestor_mapper_init_ancestors(ancestor_mapper_t *self, tsk_id_t *ancestors)
 
     /* Go through the samples to check for errors. */
     for (j = 0; j < self->num_ancestors; j++) {
-        if (ancestors[j] < 0 || ancestors[j] > (tsk_id_t) self->tables->nodes.num_rows) {
+        if (ancestors[j] < 0
+            || ancestors[j] >= (tsk_id_t) self->tables->nodes.num_rows) {
             ret = tsk_trace_error(TSK_ERR_NODE_OUT_OF_BOUNDS);
             goto out;
         }
diff --git a/python/CHANGELOG.rst b/python/CHANGELOG.rst
index 2af4a8654b..887360c8c5 100644
--- a/python/CHANGELOG.rst
+++ b/python/CHANGELOG.rst
@@ -22,6 +22,9 @@
 
 - Update to kastore C version 2.1.3 to include file security fix (:user:`jeromekelleher`, 
   :pr:`3478`).
+- ``link_ancestors`` now raises ``LibraryError`` (node out of bounds) for a sample or
+  ancestor ID equal to the number of nodes, instead of reading and writing past the
+  end of its node arrays. (:user:`asystemoffields`, :issue:`3484`, :pr:`3492`)
 
 --------------------
 [1.0.3] - 2026-05-14
diff --git a/python/tests/test_python_c.py b/python/tests/test_python_c.py
index aba3bc54cb..c594c7a38f 100644
--- a/python/tests/test_python_c.py
+++ b/python/tests/test_python_c.py
@@ -390,11 +390,16 @@ def test_link_ancestors_bad_args(self):
             tc.link_ancestors(samples=[0, 1], ancestors=[11, -1])
         with pytest.raises(_tskit.LibraryError):
             tc.link_ancestors(samples=[0, -1], ancestors=[11])
+        # One past the last node ID is out of bounds too
+        with pytest.raises(_tskit.LibraryError, match="out of bounds"):
+            tc.link_ancestors(samples=[0, tc.nodes.num_rows], ancestors=[11])
+        with pytest.raises(_tskit.LibraryError, match="out of bounds"):
+            tc.link_ancestors(samples=[0, 1], ancestors=[tc.nodes.num_rows])
 
     def test_link_ancestors(self):
         ts = msprime.simulate(2, random_seed=1)
         tc = ts.dump_tables()._ll_tables
-        edges = tc.link_ancestors([0, 1], [3])
+        edges = tc.link_ancestors([0, 1], [2])
         assert isinstance(edges, _tskit.EdgeTable)
         del edges
         assert tc.edges.num_rows == 2