diff --git a/packages/jest-haste-map/src/__tests__/__snapshots__/index-test.js.snap b/packages/jest-haste-map/src/__tests__/__snapshots__/index-test.js.snap
index 3e4a303b12c0..12bf932648b1 100644
--- a/packages/jest-haste-map/src/__tests__/__snapshots__/index-test.js.snap
+++ b/packages/jest-haste-map/src/__tests__/__snapshots__/index-test.js.snap
@@ -14,14 +14,14 @@ exports[`HasteMap tries to crawl using node as a fallback 1`] = `
 
 exports[`HasteMap warns on duplicate mock files 1`] = `
 "jest-haste-map: duplicate manual mock found:
-  Module name: blueberry
-  Duplicate Mock path: /fruits/__mocks__/subdir2/blueberry.js
+  Module name: subdir/blueberry
+  Duplicate Mock path: /fruits2/__mocks__/subdir/blueberry.js
 This warning is caused by two manual mock files with the same file name.
 Jest will use the mock file found in: 
-/fruits/__mocks__/subdir2/blueberry.js
+/fruits2/__mocks__/subdir/blueberry.js
  Please delete one of the following two files: 
- /fruits/__mocks__/subdir1/blueberry.js
-/fruits/__mocks__/subdir2/blueberry.js
+ /fruits1/__mocks__/subdir/blueberry.js
+/fruits2/__mocks__/subdir/blueberry.js
 
 "
 `;
diff --git a/packages/jest-haste-map/src/__tests__/getMockName-test.js b/packages/jest-haste-map/src/__tests__/getMockName-test.js
new file mode 100644
index 000000000000..4556e9a17018
--- /dev/null
+++ b/packages/jest-haste-map/src/__tests__/getMockName-test.js
@@ -0,0 +1,24 @@
+/**
+ * Copyright (c) 2014-present, Facebook, Inc. All rights reserved.
+ *
+ * This source code is licensed under the BSD-style license found in the
+ * LICENSE file in the root directory of this source tree. An additional grant
+ * of patent rights can be found in the PATENTS file in the same directory.
+ *
+ */
+'use strict';
+
+const path = require('path');
+const getMockName = require('../getMockName');
+
+describe('getMockName', () => {
+  it('extracts mock name from file path', () => {
+    expect(
+      getMockName(path.join('a', '__mocks__', 'c.js'))
+    ).toBe('c');
+
+    expect(
+      getMockName(path.join('a', '__mocks__', 'c', 'd.js'))
+    ).toBe(path.join('c', 'd'));
+  });
+});
diff --git a/packages/jest-haste-map/src/__tests__/index-test.js b/packages/jest-haste-map/src/__tests__/index-test.js
index 577596130859..e4079278d7e0 100644
--- a/packages/jest-haste-map/src/__tests__/index-test.js
+++ b/packages/jest-haste-map/src/__tests__/index-test.js
@@ -322,12 +322,12 @@ describe('HasteMap', () => {
 
   it('warns on duplicate mock files', () => {
     // Duplicate mock files for blueberry
-    mockFs['/fruits/__mocks__/subdir1/blueberry.js'] = [
+    mockFs['/fruits1/__mocks__/subdir/blueberry.js'] = [
       '/**',
       ' * @providesModule Blueberry1',
       ' */',
     ].join('\n');
-    mockFs['/fruits/__mocks__/subdir2/blueberry.js'] = [
+    mockFs['/fruits2/__mocks__/subdir/blueberry.js'] = [
       '/**',
       ' * @providesModule Blueberry2',
       ' */',
diff --git a/packages/jest-haste-map/src/getMockName.js b/packages/jest-haste-map/src/getMockName.js
new file mode 100644
index 000000000000..8c83081da98d
--- /dev/null
+++ b/packages/jest-haste-map/src/getMockName.js
@@ -0,0 +1,21 @@
+/**
+ * Copyright (c) 2014-present, Facebook, Inc. All rights reserved.
+ *
+ * This source code is licensed under the BSD-style license found in the
+ * LICENSE file in the root directory of this source tree. An additional grant
+ * of patent rights can be found in the PATENTS file in the same directory.
+ *
+ * @flow
+ */
+'use strict';
+
+const path = require('path');
+
+const mocksPattern = '__mocks__';
+
+const getMockName = (filePath: string) => {
+  const mockPath = filePath.split(mocksPattern)[1];
+  return mockPath.substring(1, mockPath.lastIndexOf(path.extname(mockPath)));
+};
+
+module.exports = getMockName;
diff --git a/packages/jest-haste-map/src/index.js b/packages/jest-haste-map/src/index.js
index c384e148b395..5ef784ae18c1 100644
--- a/packages/jest-haste-map/src/index.js
+++ b/packages/jest-haste-map/src/index.js
@@ -23,6 +23,7 @@ const {EventEmitter} = require('events');
 const H = require('./constants');
 const HasteFS = require('./HasteFS');
 const HasteModuleMap = require('./ModuleMap');
+const getMockName = require('./getMockName');
 
 const crypto = require('crypto');
 const execSync = require('child_process').execSync;
@@ -95,7 +96,6 @@ const canUseWatchman = ((): boolean => {
 const escapePathSeparator =
   string => (path.sep === '\\') ? string.replace(/(\/|\\)/g, '\\\\') : string;
 
-const getMockName = filePath => path.basename(filePath, path.extname(filePath));
 const getWhiteList = (list: ?Array<string>): ?RegExp => {
   if (list && list.length) {
     return new RegExp(
diff --git a/packages/jest-runtime/src/__tests__/Runtime-mock-test.js b/packages/jest-runtime/src/__tests__/Runtime-mock-test.js
index 2aaf536871f1..9a160ef8fa6a 100644
--- a/packages/jest-runtime/src/__tests__/Runtime-mock-test.js
+++ b/packages/jest-runtime/src/__tests__/Runtime-mock-test.js
@@ -9,6 +9,8 @@
  */
 'use strict';
 
+const path = require('path');
+
 let createRuntime;
 
 describe('Runtime', () => {
@@ -27,6 +29,7 @@ describe('Runtime', () => {
 
         root.jest.mock('RegularModule', () => mockReference);
         root.jest.mock('ManuallyMocked', () => mockReference);
+        root.jest.mock(path.join('nested1', 'nested2', 'nested3'));
 
         expect(
           runtime.requireModuleOrMock(runtime.__mockRootPath, 'RegularModule'),
@@ -35,6 +38,12 @@ describe('Runtime', () => {
         expect(
           runtime.requireModuleOrMock(runtime.__mockRootPath, 'ManuallyMocked'),
         ).toEqual(mockReference);
+
+        expect(
+          runtime.requireModuleOrMock(
+            runtime.__mockRootPath, path.join('nested1', 'nested2', 'nested3')
+          ),
+        ).toEqual(mockReference);
       }),
     );
 
diff --git a/packages/jest-runtime/src/__tests__/test_root/__mocks__/nested1/nested2/nested3.js b/packages/jest-runtime/src/__tests__/test_root/__mocks__/nested1/nested2/nested3.js
new file mode 100644
index 000000000000..2e6922e64cd6
--- /dev/null
+++ b/packages/jest-runtime/src/__tests__/test_root/__mocks__/nested1/nested2/nested3.js
@@ -0,0 +1,3 @@
+'use strict';
+
+exports.isMock = true;
diff --git a/packages/jest-runtime/src/__tests__/test_root/nested1/nested2/nested3.js b/packages/jest-runtime/src/__tests__/test_root/nested1/nested2/nested3.js
new file mode 100644
index 000000000000..3dec268a2c34
--- /dev/null
+++ b/packages/jest-runtime/src/__tests__/test_root/nested1/nested2/nested3.js
@@ -0,0 +1,3 @@
+'use strict';
+
+exports.isMock = false;