diff --git a/lib/matplotlib/pyplot.py b/lib/matplotlib/pyplot.py
index b8c9b88f563f..4b161c1eee05 100644
--- a/lib/matplotlib/pyplot.py
+++ b/lib/matplotlib/pyplot.py
@@ -329,8 +329,11 @@ def draw_if_interactive():
 
 
 def _warn_if_gui_out_of_main_thread():
-    if (_get_required_interactive_framework(_get_backend_mod())
-            and threading.current_thread() is not threading.main_thread()):
+    # This compares native thread ids because even if python-level Thread
+    # objects match, the underlying OS thread (which is what really matters)
+    # may be different on Python implementations with green threads.
+    if (_get_required_interactive_framework(_get_backend_mod()) and
+            threading.get_native_id() != threading.main_thread().native_id):
         _api.warn_external(
             "Starting a Matplotlib GUI outside of the main thread will likely "
             "fail.")