diff --git a/qiskit/dagcircuit/collect_blocks.py b/qiskit/dagcircuit/collect_blocks.py
index 99c51d2e3600..55587e0bc34c 100644
--- a/qiskit/dagcircuit/collect_blocks.py
+++ b/qiskit/dagcircuit/collect_blocks.py
@@ -54,7 +54,7 @@ def __init__(self, dag: DAGCircuit | DAGDependency):
 
         self.dag = dag
         self._pending_nodes: list[DAGOpNode | DAGDepNode] | None = None
-        self._in_degree: dict[DAGOpNode | DAGDepNode, int] | None = None
+        self._in_degree: dict[int, int] | None = None
         self._collect_from_back = False
 
         if isinstance(dag, DAGCircuit):
@@ -80,7 +80,7 @@ def _setup_in_degrees(self):
         self._in_degree = {}
         for node in self._op_nodes():
             deg = len(self._direct_preds(node))
-            self._in_degree[node] = deg
+            self._in_degree[self._get_node_id(node)] = deg
             if deg == 0:
                 self._pending_nodes.append(node)
 
@@ -91,6 +91,13 @@ def _op_nodes(self) -> Iterable[DAGOpNode | DAGDepNode]:
         else:
             return self.dag.get_nodes()
 
+    def _get_node_id(self, node):
+        """Returns the id of the given node."""
+        if not self.is_dag_dependency:
+            return node._node_id
+        else:
+            return node.node_id
+
     def _direct_preds(self, node):
         """Returns direct predecessors of a node. This function takes into account the
         direction of collecting blocks, that is node's predecessors when collecting
@@ -165,8 +172,8 @@ def collect_matching_block(self, filter_fn: Callable) -> list[DAGOpNode | DAGDep
 
                     # update the _in_degree of node's successors
                     for suc in self._direct_succs(node):
-                        self._in_degree[suc] -= 1
-                        if self._in_degree[suc] == 0:
+                        self._in_degree[self._get_node_id(suc)] -= 1
+                        if self._in_degree[self._get_node_id(suc)] == 0:
                             new_pending_nodes.append(suc)
                 else:
                     self._pending_nodes.append(node)
diff --git a/releasenotes/notes/fix-collect-cliffords-82b8c476e6542b36.yaml b/releasenotes/notes/fix-collect-cliffords-82b8c476e6542b36.yaml
new file mode 100644
index 000000000000..241b6a82ce5d
--- /dev/null
+++ b/releasenotes/notes/fix-collect-cliffords-82b8c476e6542b36.yaml
@@ -0,0 +1,5 @@
+---
+fixes:
+  - |
+    Fixed a problem in :class:`~BlockCollector`, by hashing the nodes using their
+    integer ids.