diff --git a/opensquirrel/passes/merger/two_qubit_gates_merger.py b/opensquirrel/passes/merger/two_qubit_gates_merger.py
index 1f8ce972..048b5c8e 100644
--- a/opensquirrel/passes/merger/two_qubit_gates_merger.py
+++ b/opensquirrel/passes/merger/two_qubit_gates_merger.py
@@ -167,18 +167,17 @@ def merge(self, ir: IR, qubit_register_size: int) -> None:
 
         """
         graph = build_graph(ir)
-        if len(graph.nodes) == 1:
-            return
-
         groups = group_gates(graph)
         statements = []
 
         for group in groups:
             statement_indices, qubit_indices = group
-            if len(qubit_indices) == 2 and len(statement_indices) > 1:
-                merged_gate = _merge_gate_group(ir, group)
-                statements.append(merged_gate)
+            if len(qubit_indices) == 2:
+                statement = _merge_gate_group(ir, group)
             else:
-                statements.append(ir.statements[statement_indices.pop()])
+                statement = ir.statements[statement_indices.pop()]
+
+            if not (isinstance(statement, Gate) and statement.is_identity()):
+                statements.append(statement)
 
         ir.statements = statements
diff --git a/tests/passes/merger/test_two_qubit_gates_merger.py b/tests/passes/merger/test_two_qubit_gates_merger.py
index 5402a88c..8f6d56f0 100644
--- a/tests/passes/merger/test_two_qubit_gates_merger.py
+++ b/tests/passes/merger/test_two_qubit_gates_merger.py
@@ -179,7 +179,6 @@ def merger() -> TwoQubitGatesMerger:
         (CircuitBuilder(1).H(0).to_circuit(), CircuitBuilder(1).H(0).to_circuit()),
         (CircuitBuilder(2).CNOT(0, 1).to_circuit(), CircuitBuilder(2).CNOT(0, 1).to_circuit()),
         (CircuitBuilder(2).CNOT(0, 1).CNOT(1, 0).CNOT(0, 1).to_circuit(), CircuitBuilder(2).SWAP(0, 1).to_circuit()),
-        (CircuitBuilder(2).SWAP(0, 1).SWAP(0, 1).to_circuit(), CircuitBuilder(2).I(0).to_circuit()),
         (CircuitBuilder(2).SWAP(0, 1).CZ(0, 1).S(0).S(1).to_circuit(), CircuitBuilder(2).ISWAP(0, 1).to_circuit()),
         (CircuitBuilder(2).H(1).CNOT(0, 1).H(1).to_circuit(), CircuitBuilder(2).CZ(0, 1).to_circuit()),
         (CircuitBuilder(2).CV(0, 1).CV(0, 1).to_circuit(), CircuitBuilder(2).CNOT(0, 1).to_circuit()),
@@ -296,3 +295,10 @@ def test_two_qubit_gates_merger_with_non_instructions(
                 "Both should be either TwoQubitGate or SingleQubitGate."
             )
             raise TypeError(msg)
+
+
+def test_two_qubit_gates_merger_filters_out_identity_gates(merger: TwoQubitGatesMerger) -> None:
+    circuit = CircuitBuilder(2).SWAP(0, 1).SWAP(0, 1).to_circuit()
+    merger.merge(circuit.ir, circuit.qubit_register_size)
+
+    assert len(circuit.ir.statements) == 0