diff --git a/java/src/main/java/org/lance/fragment/DataFile.java b/java/src/main/java/org/lance/fragment/DataFile.java
index 1120a5286c1..9755c271d67 100644
--- a/java/src/main/java/org/lance/fragment/DataFile.java
+++ b/java/src/main/java/org/lance/fragment/DataFile.java
@@ -85,7 +85,16 @@ public boolean equals(Object o) {
         && Objects.equals(path, that.path)
         && Arrays.equals(fields, that.fields)
         && Arrays.equals(columnIndices, that.columnIndices)
-        && Objects.equals(fileSizeBytes, that.fileSizeBytes);
+        && Objects.equals(fileSizeBytes, that.fileSizeBytes)
+        && Objects.equals(baseId, that.baseId);
+  }
+
+  @Override
+  public int hashCode() {
+    int result = Objects.hash(path, fileMajorVersion, fileMinorVersion, fileSizeBytes, baseId);
+    result = 31 * result + Arrays.hashCode(fields);
+    result = 31 * result + Arrays.hashCode(columnIndices);
+    return result;
   }
 
   @Override
diff --git a/java/src/main/java/org/lance/fragment/DeletionFile.java b/java/src/main/java/org/lance/fragment/DeletionFile.java
index 6fa17a37c3f..2eed2fafb0f 100644
--- a/java/src/main/java/org/lance/fragment/DeletionFile.java
+++ b/java/src/main/java/org/lance/fragment/DeletionFile.java
@@ -95,7 +95,13 @@ public boolean equals(Object o) {
     return id == that.id
         && readVersion == that.readVersion
         && fileType == that.fileType
-        && Objects.equals(numDeletedRows, that.numDeletedRows);
+        && Objects.equals(numDeletedRows, that.numDeletedRows)
+        && Objects.equals(baseId, that.baseId);
+  }
+
+  @Override
+  public int hashCode() {
+    return Objects.hash(id, readVersion, numDeletedRows, fileType, baseId);
   }
 
   @Override
diff --git a/java/src/main/java/org/lance/operation/DataOverlay.java b/java/src/main/java/org/lance/operation/DataOverlay.java
index 99abf84b797..57f5ed83f55 100644
--- a/java/src/main/java/org/lance/operation/DataOverlay.java
+++ b/java/src/main/java/org/lance/operation/DataOverlay.java
@@ -161,15 +161,7 @@ public boolean equals(Object o) {
 
     @Override
     public int hashCode() {
-      int dataFileHash =
-          Objects.hash(
-              dataFile.getPath(),
-              dataFile.getFileMajorVersion(),
-              dataFile.getFileMinorVersion(),
-              dataFile.getFileSizeBytes());
-      dataFileHash = 31 * dataFileHash + Arrays.hashCode(dataFile.getFields());
-      dataFileHash = 31 * dataFileHash + Arrays.hashCode(dataFile.getColumnIndices());
-      return Objects.hash(dataFileHash, coverage, committedVersion);
+      return Objects.hash(dataFile, coverage, committedVersion);
     }
   }
 
diff --git a/java/src/test/java/org/lance/fragment/DataFileEqualityTest.java b/java/src/test/java/org/lance/fragment/DataFileEqualityTest.java
new file mode 100644
index 00000000000..1726cda1727
--- /dev/null
+++ b/java/src/test/java/org/lance/fragment/DataFileEqualityTest.java
@@ -0,0 +1,73 @@
+/*
+ * 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 org.lance.fragment;
+
+import org.lance.FragmentMetadata;
+
+import org.junit.jupiter.api.Test;
+
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+/** Equality contract of fragment metadata value classes. */
+public class DataFileEqualityTest {
+
+  private static DataFile dataFile(Integer baseId) {
+    return new DataFile("data/a.lance", new int[] {0, 1}, new int[] {0, 1}, 2, 1, 1024L, baseId);
+  }
+
+  private static DeletionFile deletionFile(Integer baseId) {
+    return new DeletionFile(7L, 3L, 5L, DeletionFileType.BITMAP, baseId);
+  }
+
+  @Test
+  void testDataFileEqualsAndHashCodeIncludeBaseId() {
+    for (Integer baseId : new Integer[] {null, 1}) {
+      assertEquals(dataFile(baseId), dataFile(baseId));
+      assertEquals(dataFile(baseId).hashCode(), dataFile(baseId).hashCode());
+    }
+    // Same relative path under different bases refers to different physical files.
+    assertNotEquals(dataFile(1), dataFile(2));
+    assertNotEquals(dataFile(null), dataFile(1));
+  }
+
+  @Test
+  void testDeletionFileEqualsAndHashCodeIncludeBaseId() {
+    for (Integer baseId : new Integer[] {null, 1}) {
+      assertEquals(deletionFile(baseId), deletionFile(baseId));
+      assertEquals(deletionFile(baseId).hashCode(), deletionFile(baseId).hashCode());
+    }
+    assertNotEquals(deletionFile(1), deletionFile(2));
+    assertNotEquals(deletionFile(null), deletionFile(1));
+  }
+
+  @Test
+  void testEqualFragmentMetadataWorksInHashSet() {
+    FragmentMetadata a =
+        new FragmentMetadata(
+            0, Collections.singletonList(dataFile(null)), 100L, deletionFile(null), null);
+    FragmentMetadata b =
+        new FragmentMetadata(
+            0, Collections.singletonList(dataFile(null)), 100L, deletionFile(null), null);
+    assertEquals(a, b);
+    assertEquals(a.hashCode(), b.hashCode());
+    Set<FragmentMetadata> set = new HashSet<>(Collections.singletonList(a));
+    assertTrue(set.contains(b));
+  }
+}