diff --git a/packages/viewer/src/EmbeddingAtlas.svelte b/packages/viewer/src/EmbeddingAtlas.svelte
index 376434f3..530f0233 100644
--- a/packages/viewer/src/EmbeddingAtlas.svelte
+++ b/packages/viewer/src/EmbeddingAtlas.svelte
@@ -58,6 +58,7 @@
     onExportSelection,
     onStateChange,
     cache,
+    highlight: highlightProp = null,
   }: EmbeddingAtlasProps = $props();
 
   const { colorScheme, userColorScheme } = makeColorSchemeStore();
@@ -285,6 +286,23 @@
     chartThemeStore.set(chartTheme ?? undefined);
   });
 
+  // Highlight store for single point (animation + tooltip)
+  let highlightStore = writable<RowID | null>(null);
+
+  // Highlight IDs store for multiple points (overlay circles)
+  let highlightIdsStore = writable<RowID[] | null>(null);
+
+  // Sync external highlight prop to internal stores
+  $effect.pre(() => {
+    if (highlightProp != null && highlightProp.length > 0) {
+      highlightStore.set(highlightProp[0]);
+      highlightIdsStore.set(highlightProp);
+    } else {
+      highlightStore.set(null);
+      highlightIdsStore.set(null);
+    }
+  });
+
   let chartContext: ChartContext = {
     coordinator: coordinator,
     filter: crossFilter,
@@ -299,7 +317,8 @@
     searchModes: searchModes,
     search: doSearch,
     searchResult: searchResultStore,
-    highlight: writable(null),
+    highlight: highlightStore,
+    highlightIds: highlightIdsStore,
     embeddingViewConfig: embeddingViewConfig,
     embeddingViewLabels: embeddingViewLabels,
     tableCellRenderers: tableCellRenderers,
diff --git a/packages/viewer/src/api.ts b/packages/viewer/src/api.ts
index 71cc9aef..6f3fe597 100644
--- a/packages/viewer/src/api.ts
+++ b/packages/viewer/src/api.ts
@@ -87,6 +87,14 @@ export interface EmbeddingAtlasProps {
 
   /** A cache to speed up initialization of the viewer. */
   cache?: Cache | null;
+
+  /**
+   * An array of row IDs to highlight on the embedding view.
+   * When set, orange circles will be drawn at the specified points.
+   * The view will animate to show the first point in the array.
+   * Pass null or an empty array to clear the highlight.
+   */
+  highlight?: any[] | null;
 }
 
 export interface EmbeddingAtlasState {
diff --git a/packages/viewer/src/charts/chart.ts b/packages/viewer/src/charts/chart.ts
index 8a6752d8..e04edfdd 100644
--- a/packages/viewer/src/charts/chart.ts
+++ b/packages/viewer/src/charts/chart.ts
@@ -89,6 +89,9 @@ export interface ChartContext {
   /** The current highlight point. When this changes, supported views will highlight the given point. */
   highlight: Writable<RowID | null>;
 
+  /** Multiple highlight points. When set, supported views will show overlay circles at these points. */
+  highlightIds?: Readable<RowID[] | null>;
+
   /** Configuration for the embedding view. See docs for the EmbeddingView. */
   embeddingViewConfig?: EmbeddingViewConfig | null;
 
diff --git a/packages/viewer/src/charts/embedding/Embedding.svelte b/packages/viewer/src/charts/embedding/Embedding.svelte
index ef2e53f8..e5b28c8f 100644
--- a/packages/viewer/src/charts/embedding/Embedding.svelte
+++ b/packages/viewer/src/charts/embedding/Embedding.svelte
@@ -150,6 +150,33 @@
     }),
   );
 
+  // Subscribe to highlightIds for programmatic multi-point highlighting
+  $effect.pre(() => {
+    if (context.highlightIds == null) return;
+    return context.highlightIds.subscribe(async (ids) => {
+      if (ids == null || ids.length == 0) {
+        overlayProps = null;
+        return;
+      }
+      let r = Array.from(
+        await context.coordinator.query(
+          SQL.Query.from(context.table)
+            .select({ identifier: SQL.column(context.id), x: SQL.column(spec.data.x), y: SQL.column(spec.data.y) })
+            .where(
+              SQL.isIn(
+                context.id,
+                ids.map((x) => SQL.literal(x)),
+              ),
+            ),
+        ),
+      ) as DataPoint[];
+      overlayProps = {
+        center: null,
+        points: r,
+      };
+    });
+  });
+
   async function animateToPoint(identifier: RowID): Promise<void> {
     let defaultScale = await context.cache.value(`embedding/default-viewport-scale/${spec.data.x},${spec.data.y}`, () =>
       defaultViewportScale(context.coordinator, context.table, spec.data.x, spec.data.y),