diff --git a/src/mol-gl/shader/chunks/apply-marker-color.glsl b/src/mol-gl/shader/chunks/apply-marker-color.glsl
index 14741ac1666722e7f79143945a24049ffa1db11b..cc65b55255af0f62e342933641ebf6ab60c05e84 100644
--- a/src/mol-gl/shader/chunks/apply-marker-color.glsl
+++ b/src/mol-gl/shader/chunks/apply-marker-color.glsl
@@ -1,8 +1,11 @@
-float marker = vMarker * 255.0;
-if (marker > 0.1) {
-    if (mod(marker, 2.0) > 0.1) {
-        gl_FragColor.rgb = mix(uHighlightColor, gl_FragColor.rgb, 0.3);
-    } else {
-        gl_FragColor.rgb = mix(uSelectColor, gl_FragColor.rgb, 0.3);
+// only mark elements with an alpha above the picking threshold
+if (uAlpha >= uPickingAlphaThreshold) {
+    float marker = vMarker * 255.0;
+    if (marker > 0.1) {
+        if (mod(marker, 2.0) > 0.1) {
+            gl_FragColor.rgb = mix(uHighlightColor, gl_FragColor.rgb, 0.3);
+        } else {
+            gl_FragColor.rgb = mix(uSelectColor, gl_FragColor.rgb, 0.3);
+        }
     }
 }
\ No newline at end of file