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 c6875b483..9effe6022 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
@@ -1037,6 +1037,51 @@ public void testMergeRemovingFolders() throws Exception {
 		assertFalse(folder2.exists());
 	}
 
+	@Test
+	public void testMergeRemovingFoldersWithoutFastForward() throws Exception {
+		File folder1 = new File(db.getWorkTree(), "folder1");
+		File folder2 = new File(db.getWorkTree(), "folder2");
+		FileUtils.mkdir(folder1);
+		FileUtils.mkdir(folder2);
+		File file = new File(folder1, "file1.txt");
+		write(file, "folder1--file1.txt");
+		file = new File(folder1, "file2.txt");
+		write(file, "folder1--file2.txt");
+		file = new File(folder2, "file1.txt");
+		write(file, "folder--file1.txt");
+		file = new File(folder2, "file2.txt");
+		write(file, "folder2--file2.txt");
+
+		Git git = new Git(db);
+		git.add().addFilepattern(folder1.getName())
+				.addFilepattern(folder2.getName()).call();
+		RevCommit base = git.commit().setMessage("adding folders").call();
+
+		recursiveDelete(folder1);
+		recursiveDelete(folder2);
+		git.rm().addFilepattern("folder1/file1.txt")
+				.addFilepattern("folder1/file2.txt")
+				.addFilepattern("folder2/file1.txt")
+				.addFilepattern("folder2/file2.txt").call();
+		RevCommit other = git.commit()
+				.setMessage("removing folders on 'branch'").call();
+
+		git.checkout().setName(base.name()).call();
+
+		file = new File(folder2, "file3.txt");
+		write(file, "folder2--file3.txt");
+
+		git.add().addFilepattern(folder2.getName()).call();
+		git.commit().setMessage("adding another file").call();
+
+		MergeResult result = git.merge().include(other.getId())
+				.setStrategy(MergeStrategy.RESOLVE).call();
+
+		assertEquals(MergeResult.MergeStatus.MERGED,
+				result.getMergeStatus());
+		assertFalse(folder1.exists());
+	}
+
 	@Test
 	public void testFileModeMerge() throws Exception {
 		if (!FS.DETECTED.supportsExecute())
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 6130cc72c..2410d6fe0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
@@ -126,6 +126,8 @@ public enum MergeFailureReason {
 
 	private Map<String, DirCacheEntry> toBeCheckedOut = new HashMap<String, DirCacheEntry>();
 
+	private List<String> toBeDeleted = new ArrayList<String>();
+
 	private Map<String, MergeResult<? extends Sequence>> mergeResults = new HashMap<String, MergeResult<? extends Sequence>>();
 
 	private Map<String, MergeFailureReason> failingPaths = new HashMap<String, MergeFailureReason>();
@@ -240,16 +242,21 @@ private void checkout() throws NoWorkTreeException, IOException {
 			for (Map.Entry<String, DirCacheEntry> entry : toBeCheckedOut
 					.entrySet()) {
 				File f = new File(db.getWorkTree(), entry.getKey());
-				if (entry.getValue() != null) {
-					createDir(f.getParentFile());
-					DirCacheCheckout.checkoutEntry(db, f, entry.getValue(), r);
-				} else {
-					if (!f.delete())
-						failingPaths.put(entry.getKey(),
-								MergeFailureReason.COULD_NOT_DELETE);
-				}
+				createDir(f.getParentFile());
+				DirCacheCheckout.checkoutEntry(db, f, entry.getValue(), r);
 				modifiedFiles.add(entry.getKey());
 			}
+			// Iterate in reverse so that "folder/file" is deleted before
+			// "folder". Otherwise this could result in a failing path because
+			// of a non-empty directory, for which delete() would fail.
+			for (int i = toBeDeleted.size() - 1; i >= 0; i--) {
+				String fileName = toBeDeleted.get(i);
+				File f = new File(db.getWorkTree(), fileName);
+				if (!f.delete())
+					failingPaths.put(fileName,
+							MergeFailureReason.COULD_NOT_DELETE);
+				modifiedFiles.add(fileName);
+			}
 		} finally {
 			r.release();
 		}
@@ -441,7 +448,7 @@ private boolean processEntry(CanonicalTreeParser base,
 			} else if (modeT == 0 && modeB != 0) {
 				// we want THEIRS ... but THEIRS contains the deletion of the
 				// file
-				toBeCheckedOut.put(tw.getPathString(), null);
+				toBeDeleted.add(tw.getPathString());
 				return true;
 			}
 		}