diff --git a/artiq/gateware/drtio/rt_controller.py b/artiq/gateware/drtio/rt_controller.py
index 7c8183e44..ff58385ee 100644
--- a/artiq/gateware/drtio/rt_controller.py
+++ b/artiq/gateware/drtio/rt_controller.py
@@ -74,14 +74,14 @@ class RTController(Module):
         local_reset = Signal(reset=1)
         self.sync += local_reset.eq(self.csrs.reset.re)
         local_reset.attr.add("no_retiming")
-        self.clock_domains.cd_rsys = ClockDomain()
-        self.clock_domains.cd_rio = ClockDomain()
+        self.clock_domains.cd_sys_with_rst = ClockDomain()
+        self.clock_domains.cd_rtio_with_rst = ClockDomain()
         self.comb += [
-            self.cd_rsys.clk.eq(ClockSignal()),
-            self.cd_rsys.rst.eq(local_reset)
+            self.cd_sys_with_rst.clk.eq(ClockSignal()),
+            self.cd_sys_with_rst.rst.eq(local_reset)
         ]
-        self.comb += self.cd_rio.clk.eq(ClockSignal("rtio"))
-        self.specials += AsyncResetSynchronizer(self.cd_rio, local_reset)
+        self.comb += self.cd_rtio_with_rst.clk.eq(ClockSignal("rtio"))
+        self.specials += AsyncResetSynchronizer(self.cd_rtio_with_rst, local_reset)
 
         # remote channel status cache
         fifo_spaces_mem = Memory(16, channel_count)
@@ -107,7 +107,7 @@ class RTController(Module):
             )
         ]
 
-        fsm = ClockDomainsRenamer("rsys")(FSM())
+        fsm = ClockDomainsRenamer("sys_with_rst")(FSM())
         self.submodules += fsm
 
         status_wait = Signal()
@@ -120,7 +120,7 @@ class RTController(Module):
         ]
         sequence_error_set = Signal()
         underflow_set = Signal()
-        self.sync.rio += [
+        self.sync.sys_with_rst += [
             If(self.cri.cmd == cri.commands["o_underflow_reset"], status_underflow.eq(0)),
             If(self.cri.cmd == cri.commands["o_sequence_error_reset"], status_sequence_error.eq(0)),
             If(underflow_set, status_underflow.eq(1)),
@@ -128,7 +128,7 @@ class RTController(Module):
         ]
 
         signal_fifo_space_timeout = Signal()
-        self.sync += [
+        self.sync.sys_with_rst += [
             If(self.csrs.o_fifo_space_timeout.re, self.csrs.o_fifo_space_timeout.w.eq(0)),
             If(signal_fifo_space_timeout, self.csrs.o_fifo_space_timeout.w.eq(1))
         ]
diff --git a/artiq/gateware/drtio/rt_packets.py b/artiq/gateware/drtio/rt_packets.py
index 52c4261ed..efd411e1f 100644
--- a/artiq/gateware/drtio/rt_packets.py
+++ b/artiq/gateware/drtio/rt_packets.py
@@ -487,7 +487,7 @@ class RTPacketMaster(Module):
         self.submodules += rx_dp
 
         # Write FIFO and extra data count
-        wfifo = ClockDomainsRenamer({"write": "rsys", "read": "rio"})(
+        wfifo = ClockDomainsRenamer({"write": "sys_with_rst", "read": "rtio_with_rst"})(
             AsyncFIFO(64+16+16+512, write_fifo_depth))
         self.submodules += wfifo
         write_timestamp_d = Signal(64)
diff --git a/artiq/test/gateware/drtio/test_full_stack.py b/artiq/test/gateware/drtio/test_full_stack.py
index 73ff378ca..1d758c5e8 100644
--- a/artiq/test/gateware/drtio/test_full_stack.py
+++ b/artiq/test/gateware/drtio/test_full_stack.py
@@ -67,7 +67,8 @@ class DUT(Module):
 
 class TestFullStack(unittest.TestCase):
     clocks = {"sys": 8, "rtio": 5, "rtio_rx": 5,
-              "rsys": 8, "rio": 5, "rio_phy": 5}
+              "rio": 5, "rio_phy": 5,
+              "sys_with_rst": 8, "rtio_with_rst": 5}
 
     def test_controller(self):
         dut = DUT(2)