diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/MergeCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/MergeCommandTest.java
index 7efe7c948..dbf3ba015 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/MergeCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/MergeCommandTest.java
@@ -365,6 +365,48 @@ public class MergeCommandTest extends RepositoryTestCase {
 				read(new File(db.getWorkTree(), "c/c/c")));
 	}
 
+	public void testDeletionAndConflict() throws Exception {
+		Git git = new Git(db);
+
+		writeTrashFile("a", "1\na\n3\n");
+		writeTrashFile("b", "1\nb\n3\n");
+		writeTrashFile("d", "1\nd\n3\n");
+		writeTrashFile("c/c/c", "1\nc\n3\n");
+		git.add().addFilepattern("a").addFilepattern("b")
+				.addFilepattern("c/c/c").addFilepattern("d").call();
+		RevCommit initialCommit = git.commit().setMessage("initial").call();
+
+		createBranch(initialCommit, "refs/heads/side");
+		checkoutBranch("refs/heads/side");
+
+		assertTrue(new File(db.getWorkTree(), "b").delete());
+		writeTrashFile("a", "1\na\n3(side)\n");
+		git.add().addFilepattern("b").setUpdate(true).call();
+		git.add().addFilepattern("a").setUpdate(true).call();
+		RevCommit secondCommit = git.commit().setMessage("side").call();
+
+		assertFalse(new File(db.getWorkTree(), "b").exists());
+		checkoutBranch("refs/heads/master");
+		assertTrue(new File(db.getWorkTree(), "b").exists());
+
+		writeTrashFile("a", "1\na\n3(main)\n");
+		writeTrashFile("c/c/c", "1\nc(main)\n3\n");
+		git.add().addFilepattern("a").addFilepattern("c/c/c").call();
+		git.commit().setMessage("main").call();
+
+		// We are merging a deletion into our branch
+		MergeResult result = git.merge().include(secondCommit.getId())
+				.setStrategy(MergeStrategy.RESOLVE).call();
+		assertEquals(MergeStatus.CONFLICTING, result.getMergeStatus());
+
+		assertEquals(
+				"1\na\n<<<<<<< HEAD\n3(main)\n=======\n3(side)\n>>>>>>> 54ffed45d62d252715fc20e41da92d44c48fb0ff\n",
+				read(new File(db.getWorkTree(), "a")));
+		assertFalse(new File(db.getWorkTree(), "b").exists());
+		assertEquals("1\nc(main)\n3\n",
+				read(new File(db.getWorkTree(), "c/c/c")));
+	}
+
 	public void testMergeFailingWithDirtyWorkingTree() throws Exception {
 		Git git = new Git(db);
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
index a8ab433fb..1b6ec23ba 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
@@ -93,7 +93,9 @@ public class ResolveMerger extends ThreeWayMerger {
 		/** the merge failed because of a dirty index */
 		DIRTY_INDEX,
 		/** the merge failed because of a dirty workingtree */
-		DIRTY_WORKTREE
+		DIRTY_WORKTREE,
+		/** the merge failed because of a file could not be deleted */
+		COULD_NOT_DELETE
 	}
 
 	private NameConflictTreeWalk tw;
@@ -229,10 +231,16 @@ public class ResolveMerger extends ThreeWayMerger {
 	private void checkout() throws NoWorkTreeException, IOException {
 		for (Map.Entry<String, DirCacheEntry> entry : toBeCheckedOut.entrySet()) {
 			File f = new File(db.getWorkTree(), entry.getKey());
-			createDir(f.getParentFile());
-			DirCacheCheckout.checkoutEntry(db,
-					f,
-					entry.getValue(), true);
+			if (entry.getValue() != null) {
+				createDir(f.getParentFile());
+				DirCacheCheckout.checkoutEntry(db,
+						f,
+						entry.getValue(), true);
+			} else {
+				if (!f.delete())
+					failingPathes.put(entry.getKey(),
+							MergeFailureReason.COULD_NOT_DELETE);
+			}
 			modifiedFiles.add(entry.getKey());
 		}
 	}
@@ -373,13 +381,21 @@ public class ResolveMerger extends ThreeWayMerger {
 			return true;
 		}
 
-		if (nonTree(modeT) && modeB == modeO && tw.idEqual(T_BASE, T_OURS)) {
+		if (modeB == modeO && tw.idEqual(T_BASE, T_OURS)) {
 			// OURS was not changed compared to base. All changes must be in
 			// THEIRS. Choose THEIRS.
-			DirCacheEntry e=add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_0);
-			if (e!=null)
-				toBeCheckedOut.put(tw.getPathString(), e);
-			return true;
+			if (nonTree(modeT)) {
+				DirCacheEntry e = add(tw.getRawPath(), theirs,
+						DirCacheEntry.STAGE_0);
+				if (e != null)
+					toBeCheckedOut.put(tw.getPathString(), e);
+				return true;
+			} else if (modeT == 0) {
+				// we want THEIRS ... but THEIRS contains the deletion of the
+				// file
+				toBeCheckedOut.put(tw.getPathString(), null);
+				return true;
+			}
 		}
 
 		if (tw.isSubtree()) {