diff --git a/public/app/plugins/panel/geomap/layers/data/markersLayer.tsx b/public/app/plugins/panel/geomap/layers/data/markersLayer.tsx
index 918740d4324..a1773c30045 100644
--- a/public/app/plugins/panel/geomap/layers/data/markersLayer.tsx
+++ b/public/app/plugins/panel/geomap/layers/data/markersLayer.tsx
@@ -112,6 +112,7 @@ export const markersLayer: MapLayerRegistryItem<MarkersConfig> = {
       legend: legend,
       update: (data: PanelData) => {
         if (!data.series?.length) {
+          source.clear();
           return; // ignore empty
         }