diff --git a/x-pack/legacy/plugins/apm/public/components/app/ServiceMap/Cytoscape.tsx b/x-pack/legacy/plugins/apm/public/components/app/ServiceMap/Cytoscape.tsx
index 21bedc204f48b..e4b656ae8160d 100644
--- a/x-pack/legacy/plugins/apm/public/components/app/ServiceMap/Cytoscape.tsx
+++ b/x-pack/legacy/plugins/apm/public/components/app/ServiceMap/Cytoscape.tsx
@@ -14,8 +14,6 @@ import React, {
   useState
 } from 'react';
 import { debounce } from 'lodash';
-import { isRumAgentName } from '../../../../../../../plugins/apm/common/agent_name';
-import { AGENT_NAME } from '../../../../../../../plugins/apm/common/elasticsearch_fieldnames';
 import {
   animationOptions,
   cytoscapeOptions,
@@ -96,10 +94,15 @@ function getLayoutOptions(
 }
 
 function selectRoots(cy: cytoscape.Core): string[] {
-  const nodes = cy.nodes();
-  const roots = nodes.roots();
-  const rumNodes = nodes.filter(node => isRumAgentName(node.data(AGENT_NAME)));
-  return rumNodes.union(roots).map(node => node.id());
+  const bfs = cy.elements().bfs({
+    roots: cy.elements().leaves()
+  });
+  const furthestNodeFromLeaves = bfs.path.last();
+  return cy
+    .elements()
+    .roots()
+    .union(furthestNodeFromLeaves)
+    .map(el => el.id());
 }
 
 export function Cytoscape({
@@ -168,15 +171,26 @@ export function Cytoscape({
         layout.run();
       }
     };
+    let layoutstopDelayTimeout: NodeJS.Timeout;
     const layoutstopHandler: cytoscape.EventHandler = event => {
-      event.cy.animate({
-        ...animationOptions,
-        center: {
-          eles: serviceName
-            ? event.cy.getElementById(serviceName)
-            : event.cy.collection()
+      // This 0ms timer is necessary to prevent a race condition
+      // between the layout finishing rendering and viewport centering
+      layoutstopDelayTimeout = setTimeout(() => {
+        if (serviceName) {
+          event.cy.animate({
+            ...animationOptions,
+            fit: {
+              eles: event.cy.elements(),
+              padding: nodeHeight
+            },
+            center: {
+              eles: event.cy.getElementById(serviceName)
+            }
+          });
+        } else {
+          event.cy.fit(undefined, nodeHeight);
         }
-      });
+      }, 0);
     };
     // debounce hover tracking so it doesn't spam telemetry with redundant events
     const trackNodeEdgeHover = debounce(
@@ -231,6 +245,7 @@ export function Cytoscape({
         cy.removeListener('select', 'node', selectHandler);
         cy.removeListener('unselect', 'node', unselectHandler);
       }
+      clearTimeout(layoutstopDelayTimeout);
     };
   }, [cy, height, serviceName, trackApmEvent, width]);