diff --git a/c/tskit/trees.c b/c/tskit/trees.c
index 9383cbc738..c80eff7cec 100644
--- a/c/tskit/trees.c
+++ b/c/tskit/trees.c
@@ -6407,7 +6407,7 @@ tsk_treeseq_divergence_matrix_site(const tsk_treeseq_t *self, tsk_size_t num_sam
     tsk_id_t u, v;
     double left, right, span_left, span_right;
     double *restrict D;
-    tsk_size_t *mutations_per_node = malloc(num_nodes * sizeof(*mutations_per_node));
+    tsk_size_t *mutations_per_node = tsk_malloc(num_nodes * sizeof(*mutations_per_node));
 
     ret = tsk_tree_init(&tree, self, 0);
     if (ret != 0) {