diff --git a/.changeset/default-coordinate-system-selection.md b/.changeset/default-coordinate-system-selection.md
new file mode 100644
index 00000000..682f8cef
--- /dev/null
+++ b/.changeset/default-coordinate-system-selection.md
@@ -0,0 +1,5 @@
+---
+"@spatialdata/vis": patch
+---
+
+Auto-select the coordinate system when a SpatialData object has exactly one. Previously the picker started unselected (showing "Select a coordinate system") even when there was only one choice, and a separate effect would eagerly pick the first of several. Now selection defaults only in the unambiguous single-coordinate-system case; multi-system datasets still require an explicit choice.
diff --git a/packages/vis/src/SpatialCanvas/index.tsx b/packages/vis/src/SpatialCanvas/index.tsx
index 3329fb74..c2545b8e 100644
--- a/packages/vis/src/SpatialCanvas/index.tsx
+++ b/packages/vis/src/SpatialCanvas/index.tsx
@@ -457,16 +457,16 @@ function SpatialCanvasInner({
     vw,
   ]);
 
-  useEffect(() => {
-    if (coordinateSystems.length > 0 && !coordinateSystem) {
-      actions.setCoordinateSystem(coordinateSystems[0]);
-    }
-  }, [coordinateSystems, coordinateSystem, actions]);
-
   useEffect(() => {
     actions.reset();
-    if (coordinateSystem && coordinateSystems.includes(coordinateSystem)) {
-      actions.setCoordinateSystem(coordinateSystem);
+    const nextCoordinateSystem =
+      coordinateSystem && coordinateSystems.includes(coordinateSystem)
+        ? coordinateSystem
+        : coordinateSystems.length === 1
+          ? coordinateSystems[0]
+          : null;
+    if (nextCoordinateSystem) {
+      actions.setCoordinateSystem(nextCoordinateSystem);
     }
   }, [coordinateSystem, coordinateSystems, actions]);