diff --git a/frontend/javascripts/messages.tsx b/frontend/javascripts/messages.tsx
index e9e7dc996c0..855d6c22cab 100644
--- a/frontend/javascripts/messages.tsx
+++ b/frontend/javascripts/messages.tsx
@@ -503,4 +503,6 @@ instead. Only enable this option if you understand its effect. All layers will n
     `This feature is not available in your organization's plan. Ask the owner of your organization ${organizationOwnerName} to upgrade to a ${requiredPlan} plan or higher.`,
   "organization.plan.feature_not_available.owner": (requiredPlan: string) =>
     `This feature is not available in your organization's plan. Consider upgrading to a ${requiredPlan} plan or higher.`,
+  "jobs.wrongNumberOfBoundingBoxes":
+    "To use the split/merger evaluation, make sure to have exactly one bounding box, either user-defined or from a task.",
 };
diff --git a/frontend/javascripts/viewer/controller/scene_controller.ts b/frontend/javascripts/viewer/controller/scene_controller.ts
index 2bbad2759be..ecd9d887239 100644
--- a/frontend/javascripts/viewer/controller/scene_controller.ts
+++ b/frontend/javascripts/viewer/controller/scene_controller.ts
@@ -334,13 +334,18 @@ class SceneController {
      adding a new one. Since this function is executed very rarely,
      this is not a performance problem.
      */
-    for (const [tracingId, boundingBox] of Object.entries(taskCubeByTracingId)) {
+
+    // Clean up old entries
+    for (const [tracingId, _boundingBox] of Object.entries(this.taskCubeByTracingId)) {
       let taskCube = this.taskCubeByTracingId[tracingId];
-      // Remove the old box if it exists
       if (taskCube != null) {
         taskCube.getMeshes().forEach((mesh) => this.rootNode.remove(mesh));
       }
       this.taskCubeByTracingId[tracingId] = null;
+    }
+    // Add new entries
+    for (const [tracingId, boundingBox] of Object.entries(taskCubeByTracingId)) {
+      let taskCube = this.taskCubeByTracingId[tracingId];
       if (boundingBox == null || Store.getState().task == null) {
         continue;
       }
@@ -733,7 +738,7 @@ class SceneController {
         this.updateMeshesAccordingToLayerVisibility(),
       ),
       listenToStoreProperty(
-        (storeState) => getTaskBoundingBoxes(storeState.annotation),
+        (storeState) => getTaskBoundingBoxes(storeState),
         (boundingBoxesByTracingId) => this.updateTaskBoundingBoxes(boundingBoxesByTracingId),
         true,
       ),
diff --git a/frontend/javascripts/viewer/model/accessors/skeletontracing_accessor.ts b/frontend/javascripts/viewer/model/accessors/skeletontracing_accessor.ts
index 02937b11776..e273f8f1d4d 100644
--- a/frontend/javascripts/viewer/model/accessors/skeletontracing_accessor.ts
+++ b/frontend/javascripts/viewer/model/accessors/skeletontracing_accessor.ts
@@ -117,6 +117,10 @@ export function findTreeByNodeId(trees: TreeMap, nodeId: number): Tree | undefin
   return trees.values().find((tree) => tree.nodes.has(nodeId));
 }
 
+export function hasEmptyTrees(trees: TreeMap): boolean {
+  return trees.values().some((tree: Tree) => tree.nodes.size() === 0);
+}
+
 export function findTreeByName(trees: TreeMap, treeName: string): Tree | undefined {
   return trees.values().find((tree: Tree) => tree.name === treeName);
 }
diff --git a/frontend/javascripts/viewer/model/accessors/tracing_accessor.ts b/frontend/javascripts/viewer/model/accessors/tracing_accessor.ts
index 79a9c66f55c..b527d952c69 100644
--- a/frontend/javascripts/viewer/model/accessors/tracing_accessor.ts
+++ b/frontend/javascripts/viewer/model/accessors/tracing_accessor.ts
@@ -86,9 +86,10 @@ export function selectTracing(
   return tracing;
 }
 
-function _getTaskBoundingBoxes(annotation: StoreAnnotation) {
-  const layers = _.compact([annotation.skeleton, ...annotation.volumes, annotation.readOnly]);
-
+function _getTaskBoundingBoxes(state: WebknossosState) {
+  const { annotation, task } = state;
+  if (task == null) return {};
+  const layers = _.compact([annotation.skeleton, ...annotation.volumes]);
   return Object.fromEntries(layers.map((l) => [l.tracingId, l.boundingBox]));
 }
 
diff --git a/frontend/javascripts/viewer/view/action-bar/starting_job_modals.tsx b/frontend/javascripts/viewer/view/action-bar/starting_job_modals.tsx
index 264860f9929..c494ebd6fec 100644
--- a/frontend/javascripts/viewer/view/action-bar/starting_job_modals.tsx
+++ b/frontend/javascripts/viewer/view/action-bar/starting_job_modals.tsx
@@ -47,6 +47,7 @@ import {
   rgbToHex,
 } from "libs/utils";
 import _ from "lodash";
+import messages from "messages";
 import React, { useEffect, useState, useMemo } from "react";
 import { useDispatch } from "react-redux";
 import { type APIDataLayer, type APIJob, APIJobType, type VoxelSize } from "types/api_types";
@@ -56,7 +57,11 @@ import {
   getMagInfo,
   getSegmentationLayers,
 } from "viewer/model/accessors/dataset_accessor";
-import { getUserBoundingBoxesFromState } from "viewer/model/accessors/tracing_accessor";
+import { hasEmptyTrees } from "viewer/model/accessors/skeletontracing_accessor";
+import {
+  getTaskBoundingBoxes,
+  getUserBoundingBoxesFromState,
+} from "viewer/model/accessors/tracing_accessor";
 import {
   getActiveSegmentationTracingLayer,
   getReadableNameOfVolumeLayer,
@@ -636,6 +641,19 @@ function CollapsibleSplitMergerEvaluationSettings({
           children: (
             <Row>
               <Col style={{ width: "100%" }}>
+                <div style={{ marginBottom: 24 }}>
+                  You can evaluate splits/mergers on a given bounding box. <br />
+                  By default this is the user defined bounding box or the bounding box of a task.{" "}
+                  <br />
+                  Thus your annotation should contain
+                  <ul>
+                    <li> either one user defined bounding box or the bounding box of a task</li>
+                    <li>
+                      with at least one neuron (sparse) or all neurons (dense) annotated as
+                      skeletons.
+                    </li>
+                  </ul>
+                </div>
                 <Form.Item
                   layout="horizontal"
                   label="Use sparse ground truth tracing"
@@ -1054,9 +1072,10 @@ export function NucleiDetectionForm() {
 export function NeuronSegmentationForm() {
   const dataset = useWkSelector((state) => state.dataset);
   const { neuronInferralCostPerGVx } = features();
-  const hasSkeletonAnnotation = useWkSelector((state) => state.annotation.skeleton != null);
+  const skeletonAnnotation = useWkSelector((state) => state.annotation.skeleton);
   const dispatch = useDispatch();
   const [doSplitMergerEvaluation, setDoSplitMergerEvaluation] = React.useState(false);
+
   return (
     <StartJobForm
       handleClose={() => dispatch(setAIJobModalStateAction("invisible"))}
@@ -1099,6 +1118,31 @@ export function NeuronSegmentationForm() {
             doSplitMergerEvaluation,
           );
         }
+
+        const state = Store.getState();
+        const userBoundingBoxCount = getUserBoundingBoxesFromState(state).length;
+
+        if (userBoundingBoxCount > 1) {
+          Toast.error(messages["jobs.wrongNumberOfBoundingBoxes"]);
+          return;
+        }
+
+        const taskBoundingBoxes = getTaskBoundingBoxes(state);
+        if (Object.values(taskBoundingBoxes).length + userBoundingBoxCount !== 1) {
+          Toast.error(messages["jobs.wrongNumberOfBoundingBoxes"]);
+          return;
+        }
+
+        if (skeletonAnnotation == null || skeletonAnnotation.trees.size() === 0) {
+          Toast.error(
+            "Please ensure that a skeleton tree exists within the selected bounding box.",
+          );
+          return;
+        }
+        if (hasEmptyTrees(skeletonAnnotation.trees)) {
+          Toast.error("Please ensure that all skeleton trees in this annotation have some nodes.");
+          return;
+        }
         return startNeuronInferralJob(
           dataset.id,
           colorLayer.name,
@@ -1126,7 +1170,7 @@ export function NeuronSegmentationForm() {
         </>
       }
       jobSpecificInputFields={
-        hasSkeletonAnnotation && (
+        skeletonAnnotation != null && (
           <CollapsibleSplitMergerEvaluationSettings
             isActive={doSplitMergerEvaluation}
             setActive={setDoSplitMergerEvaluation}
diff --git a/unreleased_changes/8678.md b/unreleased_changes/8678.md
new file mode 100644
index 00000000000..69e9cd02160
--- /dev/null
+++ b/unreleased_changes/8678.md
@@ -0,0 +1,2 @@
+### Changed
+- Before starting a neuron segmentation with `Evaluation Settings` enabled, it is checked that a useful bounding box was selected and that some skeletons exist within the annotation, preventing the job from failing.