diff --git a/x-pack/solutions/observability/plugins/apm/public/components/app/service_map/cytoscape.test.tsx b/x-pack/solutions/observability/plugins/apm/public/components/app/service_map/cytoscape.test.tsx
new file mode 100644
index 0000000000000..1cadedede0dd0
--- /dev/null
+++ b/x-pack/solutions/observability/plugins/apm/public/components/app/service_map/cytoscape.test.tsx
@@ -0,0 +1,77 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the Elastic License
+ * 2.0; you may not use this file except in compliance with the Elastic License
+ * 2.0.
+ */
+
+import type cytoscape from 'cytoscape';
+import { filterValidElements } from './cytoscape';
+
+const node = (id: string): cytoscape.ElementDefinition => ({
+  data: { id },
+});
+
+const edge = (id: string, source: string, target: string): cytoscape.ElementDefinition => ({
+  data: { id, source, target },
+});
+
+describe('filterValidElements', () => {
+  it('returns all elements when every edge references existing nodes', () => {
+    const elements = [node('a'), node('b'), edge('a->b', 'a', 'b')];
+
+    expect(filterValidElements(elements)).toEqual(elements);
+  });
+
+  it('removes edges whose source node does not exist', () => {
+    const elements = [node('a'), edge('x->a', 'x', 'a')];
+
+    expect(filterValidElements(elements)).toEqual([node('a')]);
+  });
+
+  it('removes edges whose target node does not exist', () => {
+    const elements = [node('a'), edge('a->x', 'a', 'x')];
+
+    expect(filterValidElements(elements)).toEqual([node('a')]);
+  });
+
+  it('removes edges where both source and target nodes are missing', () => {
+    const elements = [node('a'), edge('x->y', 'x', 'y')];
+
+    expect(filterValidElements(elements)).toEqual([node('a')]);
+  });
+
+  it('keeps nodes that have no edges', () => {
+    const elements = [node('a'), node('b')];
+
+    expect(filterValidElements(elements)).toEqual(elements);
+  });
+
+  it('returns an empty array when given an empty array', () => {
+    expect(filterValidElements([])).toEqual([]);
+  });
+
+  it('handles a mix of valid and orphaned edges', () => {
+    const elements = [
+      node('a'),
+      node('b'),
+      edge('a->b', 'a', 'b'),
+      edge('a->missing', 'a', 'missing'),
+      edge('missing->b', 'missing', 'b'),
+    ];
+
+    expect(filterValidElements(elements)).toEqual([node('a'), node('b'), edge('a->b', 'a', 'b')]);
+  });
+
+  it('keeps multiple valid edges between the same nodes', () => {
+    const elements = [node('a'), node('b'), edge('e1', 'a', 'b'), edge('e2', 'a', 'b')];
+
+    expect(filterValidElements(elements)).toEqual(elements);
+  });
+
+  it('handles elements with only edges and no nodes', () => {
+    const elements = [edge('a->b', 'a', 'b')];
+
+    expect(filterValidElements(elements)).toEqual([]);
+  });
+});
diff --git a/x-pack/solutions/observability/plugins/apm/public/components/app/service_map/cytoscape.tsx b/x-pack/solutions/observability/plugins/apm/public/components/app/service_map/cytoscape.tsx
index e780f3d6bdb3d..66cb6b70921cb 100644
--- a/x-pack/solutions/observability/plugins/apm/public/components/app/service_map/cytoscape.tsx
+++ b/x-pack/solutions/observability/plugins/apm/public/components/app/service_map/cytoscape.tsx
@@ -18,6 +18,26 @@ cytoscape.use(dagre);
 
 export const CytoscapeContext = createContext<cytoscape.Core | undefined>(undefined);
 
+/**
+ * Filters out edges whose source or target node is not present in the
+ * elements list.  This prevents Cytoscape from throwing when the graph
+ * data contains inconsistencies (e.g. an edge referencing a node that
+ * was removed by server-side grouping).
+ */
+export const filterValidElements = (
+  elements: cytoscape.ElementDefinition[]
+): cytoscape.ElementDefinition[] => {
+  const nodeIds = new Set(
+    elements.filter((el) => !el.data.source && !el.data.target).map((el) => el.data.id)
+  );
+  return elements.filter((el) => {
+    if (el.data.source || el.data.target) {
+      return nodeIds.has(el.data.source) && nodeIds.has(el.data.target);
+    }
+    return true;
+  });
+};
+
 export interface CytoscapeProps {
   children?: ReactNode;
   elements: cytoscape.ElementDefinition[];
@@ -64,16 +84,18 @@ function CytoscapeComponent({ children, elements, height, serviceName, style }:
       // We do a fit if we're going from 0 to >0 elements
       const fit = cy.elements().length === 0;
 
-      cy.add(elements);
+      const validElements = filterValidElements(elements);
+
+      cy.add(validElements);
       // Remove any old elements that don't exist in the new set of elements.
-      const elementIds = elements.map((element) => element.data.id);
+      const elementIds = validElements.map((element) => element.data.id);
       cy.elements().forEach((element) => {
         if (!elementIds.includes(element.data('id'))) {
           cy.remove(element);
         } else {
           // Doing an "add" with an element with the same id will keep the original
           // element. Set the data with the new element data.
-          const newElement = elements.find((el) => el.data.id === element.id());
+          const newElement = validElements.find((el) => el.data.id === element.id());
           element.data(newElement?.data ?? element.data());
         }
       });