diff --git a/private/tools/java/rules/jvm/external/jar/MergeJars.java b/private/tools/java/rules/jvm/external/jar/MergeJars.java
index 3efe36a1..d6ce9cc7 100644
--- a/private/tools/java/rules/jvm/external/jar/MergeJars.java
+++ b/private/tools/java/rules/jvm/external/jar/MergeJars.java
@@ -118,7 +118,6 @@ public static void main(String[] args) throws IOException {
     Map<String, Path> fileToSourceJar = new TreeMap<>();
     Map<String, byte[]> fileHashCodes = new HashMap<>();

-    Set<String> createdDirectories = new HashSet<>();
     for (Path source : sources) {
       try (InputStream fis = Files.newInputStream(source);
            ZipInputStream zis = new ZipInputStream(fis)) {
@@ -144,10 +143,7 @@ public static void main(String[] args) throws IOException {
             continue;
           }

-          if (entry.isDirectory() && createdDirectories.add(entry.getName())) {
-            fileToSourceJar.put(entry.getName(), source);
-            createdDirectories.add(entry.getName());
-          } else {
+          if (!entry.isDirectory()) {
             // Duplicate files, however may not be. We need the hash to determine
             // whether we should do anything.
             byte[] hash = hash(zis);
@@ -175,6 +171,9 @@ public static void main(String[] args) throws IOException {

     // Now create the output jar
     Files.createDirectories(out.getParent());
+
+    Set<String> createdDirectories = new HashSet<>();
+
     try (OutputStream os = Files.newOutputStream(out);
          JarOutputStream jos = new JarOutputStream(os)) {
       jos.setMethod(DEFLATED);
diff --git a/tests/com/jvm/external/jar/MergeJarsTest.java b/tests/com/jvm/external/jar/MergeJarsTest.java
index 2421ff47..f9c76bbd 100644
--- a/tests/com/jvm/external/jar/MergeJarsTest.java
+++ b/tests/com/jvm/external/jar/MergeJarsTest.java
@@ -435,6 +435,26 @@ public void orderingOfAutomaticallyCreatedDirectoriesIsConduciveToSensibleUnpack
     assertTrue(indexOfQux > indexOfBaz);
   }

+  @Test
+  public void shouldCreateIntermediateDirectoriesEvenIfTheyExistInTheSourceJar() throws IOException {
+    Path input = temp.newFile("example.jar").toPath();
+    createJar(input, ImmutableMap.of(
+            "foo/", "",
+            "foo/bar", "",
+            "foo/bar/baz.txt", "cheese"));
+
+    Path output = temp.newFile("out.jar").toPath();
+
+    MergeJars.main(new String[] {
+            "--output", output.toAbsolutePath().toString(),
+            "--sources", input.toAbsolutePath().toString(),
+    });
+
+    List<String> dirNames = readDirNames(output);
+    assertTrue(dirNames.contains("foo/"));
+    assertTrue(dirNames.contains("foo/bar/"));
+  }
+
   @Test
   public void mergedJarManifestSpecialAttributesAreHandled() throws IOException {
     // This is required to allow JarInputStream to read the manifest properly
@@ -471,7 +491,9 @@ private void createJar(Path outputTo, Map<String, String> pathToContents) throws
       for (Map.Entry<String, String> entry : pathToContents.entrySet()) {
         ZipEntry ze = new StableZipEntry(entry.getKey());
         zos.putNextEntry(ze);
-        zos.write(entry.getValue().getBytes(UTF_8));
+        if (!ze.isDirectory()) {
+          zos.write(entry.getValue().getBytes(UTF_8));
+        }
         zos.closeEntry();
       }
     }