diff --git a/causallearn/utils/DAG2PAG.py b/causallearn/utils/DAG2PAG.py
index 581f5f20..9980b96b 100644
--- a/causallearn/utils/DAG2PAG.py
+++ b/causallearn/utils/DAG2PAG.py
@@ -96,12 +96,13 @@ def dag2pag(dag: Dag, islatent: List[Node]) -> GeneralGraph:
 
     data = np.empty(shape=(0, len(observed_nodes)))
     independence_test_method = CIT(data, method=d_separation, true_dag=true_dag)
-
+    node_map = PAG.get_node_map()
+    sepset_reindexed = {(node_map[nodes[i]], node_map[nodes[j]]): sepset[(i, j)] for (i, j) in sepset}
     while change_flag:
         change_flag = False
         change_flag = rulesR1R2cycle(PAG, None, change_flag, False)
-        change_flag = ruleR3(PAG, sepset, None, change_flag, False)
-        change_flag = ruleR4B(PAG, -1, data, independence_test_method, 0.05, sep_sets=sepset,
+        change_flag = ruleR3(PAG, sepset_reindexed, None, change_flag, False)
+        change_flag = ruleR4B(PAG, -1, data, independence_test_method, 0.05, sep_sets=sepset_reindexed,
                           change_flag=change_flag,
                           bk=None, verbose=False)
     return PAG