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__/index-test.js b/packages/jest-haste-map/src/__tests__/index-test.js
index 577596130859..1588890304ed 100644
--- a/packages/jest-haste-map/src/__tests__/index-test.js
+++ b/packages/jest-haste-map/src/__tests__/index-test.js
@@ -80,6 +80,18 @@ let readFileSync;
 let workerFarmMock;
 let writeFileSync;
 
+describe('getMockName', () => {
+  it('extracts mock name from file path', () => {
+    HasteMap = require('../');
+    const {getMockName} = HasteMap;
+
+    expect(getMockName('a/__b__/c.js', /__b__/)).toBe('c');
+    expect(getMockName('a/__b__/index.js', /__b__/)).toBe('index');
+    expect(getMockName('a/__b__/c/d.js', /__b__/)).toBe('c/d');
+    expect(getMockName('a/__b__/c/d/index.js', /__b__/)).toBe('c/d');
+  });
+});
+
 describe('HasteMap', () => {
   skipOnWindows.suite();
 
@@ -322,12 +334,12 @@ 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/index.js b/packages/jest-haste-map/src/index.js
index dd0d8747f642..3e8033f83b42 100644
--- a/packages/jest-haste-map/src/index.js
+++ b/packages/jest-haste-map/src/index.js
@@ -95,7 +95,14 @@ const canUseWatchman = ((): boolean => {
 const escapePathSeparator =
   string => (path.sep === '\\') ? string.replace(/(\/|\\)/g, '\\\\') : string;
 
-const getMockName = filePath => path.basename(filePath, path.extname(filePath));
+const getMockName = (filePath, mocksPattern) => {
+  const modulePath = filePath.split(mocksPattern)[1];
+  const extractMockName = new RegExp(
+    `^\\${path.sep}?(.*?)(\\${path.sep}index)?\\${path.extname(modulePath)}$`
+  );
+  return extractMockName.exec(modulePath)[1];
+};
+
 const getWhiteList = (list: ?Array<string>): ?RegExp => {
   if (list && list.length) {
     return new RegExp(
@@ -327,7 +334,7 @@ class HasteMap extends EventEmitter {
       this._options.mocksPattern &&
       this._options.mocksPattern.test(filePath)
     ) {
-      const mockPath = getMockName(filePath);
+      const mockPath = getMockName(filePath, this._options.mocksPattern);
       if (mocks[mockPath]) {
         this._console.warn(
           `jest-haste-map: duplicate manual mock found:\n` +
@@ -617,7 +624,7 @@ class HasteMap extends EventEmitter {
           this._options.mocksPattern &&
           this._options.mocksPattern.test(filePath)
         ) {
-          const mockName = getMockName(filePath);
+          const mockName = getMockName(filePath, this._options.mocksPattern);
           delete hasteMap.mocks[mockName];
         }
 
@@ -701,8 +708,11 @@ class HasteMap extends EventEmitter {
   }
 
   static H: HType;
+
+  static getMockName;
 }
 
 HasteMap.H = H;
+HasteMap.getMockName = getMockName;
 
 module.exports = HasteMap;
diff --git a/packages/jest-runtime/src/__tests__/Runtime-mock-test.js b/packages/jest-runtime/src/__tests__/Runtime-mock-test.js
index ffd54a819252..d20410399c4a 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, 'RegularModule'),
         ).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;