diff --git a/src/main/java/com/google/devtools/build/lib/skyframe/ArtifactFunction.java b/src/main/java/com/google/devtools/build/lib/skyframe/ArtifactFunction.java
index 8e3adbe..326e331 100644
--- a/src/main/java/com/google/devtools/build/lib/skyframe/ArtifactFunction.java
+++ b/src/main/java/com/google/devtools/build/lib/skyframe/ArtifactFunction.java
@@ -637,6 +637,11 @@
     }
 
     @Override
+    protected boolean emitEmptyDirectoryNodes() {
+      return true;
+    }
+
+    @Override
     protected String errorInfo() {
       return "Directory artifact " + artifact.prettyPrint();
     }
diff --git a/src/main/java/com/google/devtools/build/lib/skyframe/FilesetTraversalRequest.java b/src/main/java/com/google/devtools/build/lib/skyframe/FilesetTraversalRequest.java
index 650c21b..e98ff06 100644
--- a/src/main/java/com/google/devtools/build/lib/skyframe/FilesetTraversalRequest.java
+++ b/src/main/java/com/google/devtools/build/lib/skyframe/FilesetTraversalRequest.java
@@ -65,6 +65,11 @@
   }
 
   @Override
+  protected boolean emitEmptyDirectoryNodes() {
+    return false;
+  }
+
+  @Override
   protected final String errorInfo() {
     return String.format(
         "Fileset '%s' traversing %s '%s'",
diff --git a/src/main/java/com/google/devtools/build/lib/skyframe/RecursiveFilesystemTraversalFunction.java b/src/main/java/com/google/devtools/build/lib/skyframe/RecursiveFilesystemTraversalFunction.java
index a50cc3f..de37dd5 100644
--- a/src/main/java/com/google/devtools/build/lib/skyframe/RecursiveFilesystemTraversalFunction.java
+++ b/src/main/java/com/google/devtools/build/lib/skyframe/RecursiveFilesystemTraversalFunction.java
@@ -620,6 +620,9 @@
       paths = NestedSetBuilder.<ResolvedFile>stableOrder().addTransitive(children).add(root);
     } else {
       root = ResolvedFileFactory.directory(rootInfo.realPath);
+      if (traversal.emitEmptyDirectoryNodes() && paths.isEmpty()) {
+        paths.add(root);
+      }
     }
     return RecursiveFilesystemTraversalValue.of(root, paths.build());
   }
diff --git a/src/main/java/com/google/devtools/build/lib/skyframe/TraversalRequest.java b/src/main/java/com/google/devtools/build/lib/skyframe/TraversalRequest.java
index 55871f1..2073b72 100644
--- a/src/main/java/com/google/devtools/build/lib/skyframe/TraversalRequest.java
+++ b/src/main/java/com/google/devtools/build/lib/skyframe/TraversalRequest.java
@@ -53,6 +53,14 @@
   protected abstract boolean skipTestingForSubpackage();
 
   /**
+   * Whether to emit nodes for empty directories.
+   *
+   * <p>If this returns false, empty directories will not be represented in the result of the
+   * traversal.
+   */
+  protected abstract boolean emitEmptyDirectoryNodes();
+
+  /**
    * Returns information to be attached to any error messages that may be reported.
    *
    * <p>This is purely informational and is not considered in equality.
diff --git a/src/test/java/com/google/devtools/build/lib/skyframe/BUILD b/src/test/java/com/google/devtools/build/lib/skyframe/BUILD
index b6806de..716067f 100644
--- a/src/test/java/com/google/devtools/build/lib/skyframe/BUILD
+++ b/src/test/java/com/google/devtools/build/lib/skyframe/BUILD
@@ -20,6 +20,7 @@
     "SkyframeErrorProcessorTest.java",
     "BuildDriverFunctionTest.java",
     "SkyFunctionEnvironmentForTesting.java",
+    "TrackSourceDirectoriesIntegrationTest.java",
 ]
 
 java_library(
@@ -433,3 +434,22 @@
         "//third_party:truth",
     ],
 )
+
+java_test(
+    name = "TrackSourceDirectoriesIntegrationTest",
+    srcs = ["TrackSourceDirectoriesIntegrationTest.java"],
+    jvm_flags = ["-DBAZEL_TRACK_SOURCE_DIRECTORIES=1"],
+    deps = [
+        "//src/main/java/com/google/devtools/build/lib/events",
+        "//src/main/java/com/google/devtools/build/lib/skyframe:track_source_directories_flag",
+        "//src/main/java/com/google/devtools/build/lib/vfs",
+        "//src/test/java/com/google/devtools/build/lib/buildtool/util",
+        "//src/test/java/com/google/devtools/build/lib/events:testutil",
+        "//src/test/java/com/google/devtools/build/lib/testutil:JunitUtils",
+        "//src/test/java/com/google/devtools/build/skyframe:testutil",
+        "//third_party:guava",
+        "//third_party:junit4",
+        "//third_party:truth",
+        "@com_google_testparameterinjector//:testparameterinjector",
+    ],
+)
diff --git a/src/test/java/com/google/devtools/build/lib/skyframe/RecursiveFilesystemTraversalFunctionTest.java b/src/test/java/com/google/devtools/build/lib/skyframe/RecursiveFilesystemTraversalFunctionTest.java
index 166ca3a..2275716 100644
--- a/src/test/java/com/google/devtools/build/lib/skyframe/RecursiveFilesystemTraversalFunctionTest.java
+++ b/src/test/java/com/google/devtools/build/lib/skyframe/RecursiveFilesystemTraversalFunctionTest.java
@@ -64,6 +64,7 @@
 import com.google.devtools.build.lib.skyframe.RecursiveFilesystemTraversalFunction.DanglingSymlinkException;
 import com.google.devtools.build.lib.skyframe.RecursiveFilesystemTraversalFunction.RecursiveFilesystemTraversalException;
 import com.google.devtools.build.lib.skyframe.RecursiveFilesystemTraversalValue.ResolvedFile;
+import com.google.devtools.build.lib.skyframe.RecursiveFilesystemTraversalValue.ResolvedFileFactory;
 import com.google.devtools.build.lib.testutil.FoundationTestCase;
 import com.google.devtools.build.lib.testutil.TimestampGranularityUtils;
 import com.google.devtools.build.lib.util.io.OutErr;
@@ -304,13 +305,22 @@
   }
 
   private static TraversalRequest fileLikeRoot(
-      Artifact file, PackageBoundaryMode pkgBoundaryMode, boolean strictOutput) {
+      Artifact file,
+      PackageBoundaryMode pkgBoundaryMode,
+      boolean strictOutput,
+      boolean emitEmptyDirectoryNodes) {
     return new AutoValue_RecursiveFilesystemTraversalFunctionTest_BasicTraversalRequest(
         DirectTraversalRoot.forFileOrDirectory(file),
         /*isRootGenerated=*/ !file.isSourceArtifact(),
         pkgBoundaryMode,
         strictOutput,
-        /*skipTestingForSubpackage=*/ false);
+        /*skipTestingForSubpackage=*/ false,
+        emitEmptyDirectoryNodes);
+  }
+
+  private static TraversalRequest fileLikeRoot(
+      Artifact file, PackageBoundaryMode pkgBoundaryMode, boolean strictOutput) {
+    return fileLikeRoot(file, pkgBoundaryMode, strictOutput, /*emitEmptyDirectoryNodes=*/ false);
   }
 
   private static TraversalRequest fileLikeRoot(Artifact file, PackageBoundaryMode pkgBoundaryMode) {
@@ -324,7 +334,8 @@
         /*isRootGenerated=*/ false,
         pkgBoundaryMode,
         /*strictOutputFiles=*/ false,
-        /*skipTestingForSubpackage=*/ true);
+        /*skipTestingForSubpackage=*/ true,
+        /*emitEmptyDirectoryNodes=*/ false);
   }
 
   @AutoValue
@@ -343,7 +354,8 @@
           isRootGenerated(),
           crossPkgBoundaries(),
           strictOutputFiles(),
-          skipTestingForSubpackage);
+          skipTestingForSubpackage,
+          emitEmptyDirectoryNodes());
     }
   }
 
@@ -671,9 +683,29 @@
     appendToFile(someFile, "not all changes are treated equal");
     RecursiveFilesystemTraversalValue v4 =
         traverseAndAssertFiles(traversalRoot, expected1, expected2, expected3);
-    assertThat(v4).isEqualTo(v3);
+    assertThat(v4).isSameInstanceAs(v3);
     assertTraversalRootHashesAreEqual(v3, v4);
     assertThat(progressReceiver.invalidations).doesNotContain(traversalRoot);
+
+    // Add a new empty subdirectory to the directory and see that the value is rebuilt, but results
+    // in the collection of files.
+    // TODO(#15901): Empty directories currently aren't representable as tree artifact contents and
+    //  thus aren't tested here.
+    if (!directoryArtifact.isTreeArtifact()) {
+      childOf(directoryArtifact, "empty_dir").asPath().createDirectory();
+      if (directoryArtifact.isSourceArtifact()) {
+        invalidateDirectory(directoryArtifact);
+      } else {
+        invalidateOutputArtifact(directoryArtifact);
+      }
+
+      RecursiveFilesystemTraversalValue v5 =
+          traverseAndAssertFiles(traversalRoot, expected1, expected2, expected3);
+      assertThat(v5.getResolvedRoot()).isEqualTo(v4.getResolvedRoot());
+      assertThat(v5.getTransitiveFiles().toList())
+          .containsExactlyElementsIn(v4.getTransitiveFiles().toList());
+      assertThat(progressReceiver.invalidations).contains(traversalRoot);
+    }
   }
 
   @Test
@@ -694,6 +726,43 @@
   }
 
   @Test
+  public void testTraversalOfSourceDirectoryWithEmptyDirectoryNodes() throws Exception {
+    Artifact directoryArtifact = sourceArtifact("dir");
+    directoryArtifact.getPath().createDirectoryAndParents();
+
+    TraversalRequest traversalRoot =
+        fileLikeRoot(
+            directoryArtifact,
+            DONT_CROSS,
+            /*strictOutput=*/ false,
+            /*emitEmptyDirectoryNodes=*/ true);
+
+    // Assert that the SkyValue is built and looks right.
+    ResolvedFile rootNode =
+        ResolvedFileFactory.directory(
+            RootedPath.toRootedPath(
+                directoryArtifact.getRoot().getRoot(), directoryArtifact.getRootRelativePath()));
+    RecursiveFilesystemTraversalValue v1 = traverseAndAssertFiles(traversalRoot, rootNode);
+    assertThat(progressReceiver.invalidations).isEmpty();
+    assertThat(progressReceiver.evaluations).contains(traversalRoot);
+    progressReceiver.clear();
+
+    // Add a new file to the directory and see that the value is rebuilt.
+    RootedPath emptyDir = childOf(directoryArtifact, "empty_dir");
+    emptyDir.asPath().createDirectory();
+    ResolvedFile emptyDirNode = ResolvedFileFactory.directory(emptyDir);
+    invalidateDirectory(directoryArtifact);
+
+    // The value only contains nodes for empty directories - the root dir is no longer empty at this
+    // point and thus not represented as a node.
+    RecursiveFilesystemTraversalValue v2 = traverseAndAssertFiles(traversalRoot, emptyDirNode);
+    assertThat(v2).isNotEqualTo(v1);
+    assertTraversalRootHashesAreEqual(v1, v2);
+    assertThat(progressReceiver.invalidations).contains(traversalRoot);
+    assertThat(progressReceiver.evaluations).contains(traversalRoot);
+  }
+
+  @Test
   public void testTraversalOfTransitiveSymlinkToDirectory() throws Exception {
     Artifact directLinkArtifact = sourceArtifact("direct/dir.sym");
     Artifact transitiveLinkArtifact = sourceArtifact("transitive/sym.sym");
diff --git a/src/test/java/com/google/devtools/build/lib/skyframe/TrackSourceDirectoriesIntegrationTest.java b/src/test/java/com/google/devtools/build/lib/skyframe/TrackSourceDirectoriesIntegrationTest.java
new file mode 100644
index 0000000..f9534f4
--- /dev/null
+++ b/src/test/java/com/google/devtools/build/lib/skyframe/TrackSourceDirectoriesIntegrationTest.java
@@ -0,0 +1,139 @@
+// Copyright 2022 The Bazel Authors. All rights reserved.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//    http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+package com.google.devtools.build.lib.skyframe;
+
+import static com.google.common.truth.Truth.assertThat;
+import static com.google.devtools.build.lib.testutil.MoreAsserts.assertContainsEvent;
+import static com.google.devtools.build.lib.testutil.MoreAsserts.assertDoesNotContainEvent;
+
+import com.google.common.collect.ImmutableSet;
+import com.google.devtools.build.lib.buildtool.util.BuildIntegrationTestCase;
+import com.google.devtools.build.lib.events.EventKind;
+import com.google.devtools.build.lib.events.util.EventCollectionApparatus;
+import com.google.devtools.build.lib.vfs.FileSystemUtils;
+import com.google.devtools.build.lib.vfs.Path;
+import com.google.testing.junit.testparameterinjector.TestParameter;
+import com.google.testing.junit.testparameterinjector.TestParameterInjector;
+import java.io.IOException;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+
+/** Tests for {@link TrackSourceDirectoriesFlag}. */
+@RunWith(TestParameterInjector.class)
+public final class TrackSourceDirectoriesIntegrationTest extends BuildIntegrationTestCase {
+
+  @Override
+  protected EventCollectionApparatus createEvents() {
+    return new EventCollectionApparatus(ImmutableSet.of(EventKind.FINISH));
+  }
+
+  @BeforeClass
+  public static void checkTrackSourceDirectoriesFlag() {
+    // Enabled via jvm_flags.
+    assertThat(TrackSourceDirectoriesFlag.trackSourceDirectories()).isTrue();
+  }
+
+  @Test
+  public void build_unchangedSourceDirectory_doesNotRebuild() throws Exception {
+    getWorkspace().getRelative("pkg/dir/empty_dir").createDirectoryAndParents();
+    write("pkg/dir/file", "foo");
+    write(
+        "pkg/BUILD",
+        "genrule(",
+        "    name = 'a',",
+        "    srcs = ['dir'],",
+        "    outs = ['out'],",
+        "    cmd = 'touch $@',",
+        ")");
+
+    String testTarget = "//pkg:a";
+    String testTargetRebuildsEvent = "Executing genrule " + testTarget;
+
+    // Initial build
+    buildTarget(testTarget);
+    assertContainsEvent(events.collector(), testTargetRebuildsEvent);
+    events.collector().clear();
+
+    // Verify that the target doesn't rebuild without changes.
+    buildTarget(testTarget);
+
+    assertDoesNotContainEvent(events.collector(), testTargetRebuildsEvent);
+  }
+
+  private enum Change {
+    CREATE_EMPTY_DIRECTORY {
+      @Override
+      void apply(Path sourceDirectory) throws IOException {
+        sourceDirectory.getRelative("empty_dir/nested_empty_dir").createDirectory();
+      }
+    },
+    CREATE_EMPTY_FILE_IN_EMPTY_DIRECTORY {
+      @Override
+      void apply(Path sourceDirectory) throws IOException {
+        FileSystemUtils.createEmptyFile(sourceDirectory.getRelative("empty_dir/file"));
+      }
+    },
+    REMOVE_EMPTY_DIRECTORY {
+      @Override
+      void apply(Path sourceDirectory) throws IOException {
+        sourceDirectory.getChild("empty_dir").deleteTree();
+      }
+    },
+    REPLACE_EMPTY_DIRECTORY_WITH_EMPTY_FILE {
+      @Override
+      void apply(Path sourceDirectory) throws IOException {
+        sourceDirectory.getChild("empty_dir").deleteTree();
+        FileSystemUtils.createEmptyFile(sourceDirectory.getChild("empty_dir"));
+      }
+    },
+    CHANGE_FILE_CONTENT {
+      @Override
+      void apply(Path sourceDirectory) throws IOException {
+        FileSystemUtils.writeContentAsLatin1(sourceDirectory.getChild("file"), "changed");
+      }
+    };
+
+    abstract void apply(Path sourceDirectory) throws IOException;
+  }
+
+  @Test
+  public void build_changedSourceDirectory_rebuildsTarget(@TestParameter Change change)
+      throws Exception {
+    getWorkspace().getRelative("pkg/dir/empty_dir").createDirectoryAndParents();
+    write("pkg/dir/file", "foo");
+    write(
+        "pkg/BUILD",
+        "genrule(",
+        "    name = 'a',",
+        "    srcs = ['dir'],",
+        "    outs = ['out'],",
+        "    cmd = 'touch $@',",
+        ")");
+
+    String testTarget = "//pkg:a";
+    String testTargetRebuildsEvent = "Executing genrule " + testTarget;
+
+    // Initial build
+    buildTarget(testTarget);
+    assertContainsEvent(events.collector(), testTargetRebuildsEvent);
+    events.collector().clear();
+
+    // Change source directory and verify that the target is rebuilt as expected.
+    change.apply(getWorkspace().getRelative("pkg/dir"));
+    buildTarget(testTarget);
+
+    assertContainsEvent(events.collector(), testTargetRebuildsEvent);
+  }
+}