diff --git a/editor/plugins/tiles/tile_map_layer_editor.cpp b/editor/plugins/tiles/tile_map_layer_editor.cpp
index c7c1ae769edf..c00a6d99d3a5 100644
--- a/editor/plugins/tiles/tile_map_layer_editor.cpp
+++ b/editor/plugins/tiles/tile_map_layer_editor.cpp
@@ -1846,7 +1846,8 @@ void TileMapLayerEditorTilesPlugin::_tile_atlas_control_draw() {
 	Color grid_color = EDITOR_GET("editors/tiles_editor/grid_color");
 	Color selection_color = Color().from_hsv(Math::fposmod(grid_color.get_h() + 0.5, 1.0), grid_color.get_s(), grid_color.get_v(), 1.0);
 	for (const TileMapCell &E : tile_set_selection) {
-		if (E.source_id == source_id && E.alternative_tile == 0) {
+		int16_t untransformed_alternative_id = E.alternative_tile & TileSetAtlasSource::UNTRANSFORM_MASK;
+		if (E.source_id == source_id && untransformed_alternative_id == 0) {
 			for (int frame = 0; frame < atlas->get_tile_animation_frames_count(E.get_atlas_coords()); frame++) {
 				Color color = selection_color;
 				if (frame > 0) {
@@ -2029,8 +2030,9 @@ void TileMapLayerEditorTilesPlugin::_tile_alternatives_control_draw() {
 
 	// Draw the selection.
 	for (const TileMapCell &E : tile_set_selection) {
-		if (E.source_id == source_id && E.get_atlas_coords() != TileSetSource::INVALID_ATLAS_COORDS && E.alternative_tile > 0) {
-			Rect2i rect = tile_atlas_view->get_alternative_tile_rect(E.get_atlas_coords(), E.alternative_tile);
+		int16_t untransformed_alternative_id = E.alternative_tile & TileSetAtlasSource::UNTRANSFORM_MASK;
+		if (E.source_id == source_id && E.get_atlas_coords() != TileSetSource::INVALID_ATLAS_COORDS && untransformed_alternative_id > 0) {
+			Rect2i rect = tile_atlas_view->get_alternative_tile_rect(E.get_atlas_coords(), untransformed_alternative_id);
 			if (rect != Rect2i()) {
 				TilesEditorUtils::draw_selection_rect(alternative_tiles_control, rect);
 			}
diff --git a/scene/resources/2d/tile_set.h b/scene/resources/2d/tile_set.h
index f1a8d42b95a3..dceda1a791c3 100644
--- a/scene/resources/2d/tile_set.h
+++ b/scene/resources/2d/tile_set.h
@@ -619,6 +619,8 @@ class TileSetAtlasSource : public TileSetSource {
 		TRANSFORM_TRANSPOSE = 1 << 14,
 	};
 
+	static const int16_t UNTRANSFORM_MASK = ~(TileSetAtlasSource::TRANSFORM_FLIP_H + TileSetAtlasSource::TRANSFORM_FLIP_V + TileSetAtlasSource::TRANSFORM_TRANSPOSE);
+
 private:
 	struct TileAlternativesData {
 		Vector2i size_in_atlas = Vector2i(1, 1);