diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
index 164da3f1d..307d947f3 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
@@ -143,6 +143,7 @@ protected void run() throws Exception {
 			revision = null;
 		}
 
+		boolean autoAbbrev = abbrev == 0;
 		if (abbrev == 0)
 			abbrev = db.getConfig().getInt("core", "abbrev", 7); //$NON-NLS-1$ //$NON-NLS-2$
 		if (!showBlankBoundary)
@@ -156,6 +157,7 @@ protected void run() throws Exception {
 			dateFmt = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss ZZZZ"); //$NON-NLS-1$
 
 		BlameGenerator generator = new BlameGenerator(db, file);
+		RevFlag scanned = generator.newFlag("SCANNED"); //$NON-NLS-1$
 		reader = db.newObjectReader();
 		try {
 			generator.setTextComparator(comparator);
@@ -198,9 +200,17 @@ protected void run() throws Exception {
 			int pathWidth = 1;
 			int maxSourceLine = 1;
 			for (int line = begin; line < end; line++) {
-				authorWidth = Math.max(authorWidth, author(line).length());
-				dateWidth = Math.max(dateWidth, date(line).length());
-				pathWidth = Math.max(pathWidth, path(line).length());
+				RevCommit c = blame.getSourceCommit(line);
+				if (c != null && !c.has(scanned)) {
+					c.add(scanned);
+					if (autoAbbrev)
+						abbrev = Math.max(abbrev, uniqueAbbrevLen(c));
+					authorWidth = Math.max(authorWidth, author(line).length());
+					dateWidth = Math.max(dateWidth, date(line).length());
+					pathWidth = Math.max(pathWidth, path(line).length());
+				}
+				while (line + 1 < end && blame.getSourceCommit(line + 1) == c)
+					line++;
 				maxSourceLine = Math.max(maxSourceLine, blame.getSourceLine(line));
 			}
 
@@ -232,6 +242,10 @@ protected void run() throws Exception {
 		}
 	}
 
+	private int uniqueAbbrevLen(RevCommit commit) throws IOException {
+		return reader.abbreviate(commit, abbrev).length();
+	}
+
 	private void parseLineRangeOption() {
 		String beginStr, endStr;
 		if (rangeString.startsWith("/")) { //$NON-NLS-1$
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/BlameCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/BlameCommandTest.java
index 20e93f88c..743e16de0 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/BlameCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/BlameCommandTest.java
@@ -386,4 +386,74 @@ private void testCoreAutoCrlf(AutoCRLF modeForCommitting,
 		assertEquals(commit, lines.getSourceCommit(1));
 		assertEquals(commit, lines.getSourceCommit(2));
 	}
+
+	@Test
+	public void testConflictingMerge1() throws Exception {
+		Git git = new Git(db);
+
+		RevCommit base = commitFile("file.txt", join("0", "1", "2", "3", "4"),
+				"master");
+
+		git.checkout().setName("side").setCreateBranch(true)
+				.setStartPoint(base).call();
+		RevCommit side = commitFile("file.txt",
+				join("0", "1 side", "2", "3 on side", "4"), "side");
+
+		commitFile("file.txt", join("0", "1", "2"), "master");
+
+		checkoutBranch("refs/heads/master");
+		git.merge().include(side).call();
+
+		// The merge results in a conflict, which we resolve using mostly the
+		// side branch contents. Especially the "4" survives.
+		RevCommit merge = commitFile("file.txt",
+				join("0", "1 side", "2", "3 resolved", "4"), "master");
+
+		BlameCommand command = new BlameCommand(db);
+		command.setFilePath("file.txt");
+		BlameResult lines = command.call();
+
+		assertEquals(5, lines.getResultContents().size());
+		assertEquals(base, lines.getSourceCommit(0));
+		assertEquals(side, lines.getSourceCommit(1));
+		assertEquals(base, lines.getSourceCommit(2));
+		assertEquals(merge, lines.getSourceCommit(3));
+		assertEquals(base, lines.getSourceCommit(4));
+	}
+
+	// this test inverts the order of the master and side commit and is
+	// otherwise identical to testConflictingMerge1
+	@Test
+	public void testConflictingMerge2() throws Exception {
+		Git git = new Git(db);
+
+		RevCommit base = commitFile("file.txt", join("0", "1", "2", "3", "4"),
+				"master");
+
+		commitFile("file.txt", join("0", "1", "2"), "master");
+
+		git.checkout().setName("side").setCreateBranch(true)
+				.setStartPoint(base).call();
+		RevCommit side = commitFile("file.txt",
+				join("0", "1 side", "2", "3 on side", "4"), "side");
+
+		checkoutBranch("refs/heads/master");
+		git.merge().include(side).call();
+
+		// The merge results in a conflict, which we resolve using mostly the
+		// side branch contents. Especially the "4" survives.
+		RevCommit merge = commitFile("file.txt",
+				join("0", "1 side", "2", "3 resolved", "4"), "master");
+
+		BlameCommand command = new BlameCommand(db);
+		command.setFilePath("file.txt");
+		BlameResult lines = command.call();
+
+		assertEquals(5, lines.getResultContents().size());
+		assertEquals(base, lines.getSourceCommit(0));
+		assertEquals(side, lines.getSourceCommit(1));
+		assertEquals(base, lines.getSourceCommit(2));
+		assertEquals(merge, lines.getSourceCommit(3));
+		assertEquals(base, lines.getSourceCommit(4));
+	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/blame/BlameGenerator.java b/org.eclipse.jgit/src/org/eclipse/jgit/blame/BlameGenerator.java
index b7ad9d1a1..5b02ce6c9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/blame/BlameGenerator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/blame/BlameGenerator.java
@@ -44,6 +44,7 @@
 package org.eclipse.jgit.blame;
 
 import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
+import static org.eclipse.jgit.lib.FileMode.TYPE_FILE;
 
 import java.io.IOException;
 import java.util.Collection;
@@ -72,6 +73,7 @@
 import org.eclipse.jgit.revwalk.RevFlag;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.treewalk.TreeWalk;
+import org.eclipse.jgit.treewalk.filter.AndTreeFilter;
 import org.eclipse.jgit.treewalk.filter.PathFilter;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
 
@@ -121,7 +123,7 @@ public class BlameGenerator {
 	/** Revision pool used to acquire commits from. */
 	private RevWalk revPool;
 
-	/** Indicates the commit has already been processed. */
+	/** Indicates the commit was put into the queue at least once. */
 	private RevFlag SEEN;
 
 	private ObjectReader reader;
@@ -146,7 +148,7 @@ public class BlameGenerator {
 	/**
 	 * Create a blame generator for the repository and path (relative to
 	 * repository)
-	 * 
+	 *
 	 * @param repository
 	 *            repository to access revision data from.
 	 * @param path
@@ -422,6 +424,18 @@ public BlameGenerator reverse(AnyObjectId start,
 		return this;
 	}
 
+	/**
+	 * Allocate a new RevFlag for use by the caller.
+	 *
+	 * @param name
+	 *            unique name of the flag in the blame context.
+	 * @return the newly allocated flag.
+	 * @since 3.4
+	 */
+	public RevFlag newFlag(String name) {
+		return revPool.newFlag(name);
+	}
+
 	/**
 	 * Execute the generator in a blocking fashion until all data is ready.
 	 *
@@ -532,6 +546,7 @@ private Candidate pop() {
 	private void push(BlobCandidate toInsert) {
 		Candidate c = queue;
 		if (c != null) {
+			c.remove(SEEN); // will be pushed by toInsert
 			c.regionList = null;
 			toInsert.parent = c;
 		}
@@ -539,8 +554,24 @@ private void push(BlobCandidate toInsert) {
 	}
 
 	private void push(Candidate toInsert) {
-		// Mark sources to ensure they get discarded (above) if
-		// another path to the same commit.
+		if (toInsert.has(SEEN)) {
+			// We have already added a Candidate for this commit to the queue,
+			// this can happen if the commit is a merge base for two or more
+			// parallel branches that were merged together.
+			//
+			// It is likely the candidate was not yet processed. The queue
+			// sorts descending by commit time and usually descendant commits
+			// have higher timestamps than the ancestors.
+			//
+			// Find the existing candidate and merge the new candidate's
+			// region list into it.
+			for (Candidate p = queue; p != null; p = p.queueNext) {
+				if (p.canMergeRegions(toInsert)) {
+					p.mergeRegions(toInsert);
+					return;
+				}
+			}
+		}
 		toInsert.add(SEEN);
 
 		// Insert into the queue using descending commit time, so
@@ -567,23 +598,21 @@ private boolean processOne(Candidate n) throws IOException {
 		RevCommit parent = n.getParent(0);
 		if (parent == null)
 			return split(n.getNextCandidate(0), n);
-		if (parent.has(SEEN))
-			return false;
 		revPool.parseHeaders(parent);
 
-		if (find(parent, n.sourcePath)) {
-			if (idBuf.equals(n.sourceBlob)) {
-				// The common case of the file not being modified in
-				// a simple string-of-pearls history. Blame parent.
-				n.sourceCommit = parent;
-				push(n);
-				return false;
+		if (n.sourceCommit != null && n.recursivePath) {
+			treeWalk.setFilter(AndTreeFilter.create(n.sourcePath, ID_DIFF));
+			treeWalk.reset(n.sourceCommit.getTree(), parent.getTree());
+			if (!treeWalk.next())
+				return blameEntireRegionOnParent(n, parent);
+			if (isFile(treeWalk.getRawMode(1))) {
+				treeWalk.getObjectId(idBuf, 1);
+				return splitBlameWithParent(n, parent);
 			}
-
-			Candidate next = n.create(parent, n.sourcePath);
-			next.sourceBlob = idBuf.toObjectId();
-			next.loadText(reader);
-			return split(next, n);
+		} else if (find(parent, n.sourcePath)) {
+			if (idBuf.equals(n.sourceBlob))
+				return blameEntireRegionOnParent(n, parent);
+			return splitBlameWithParent(n, parent);
 		}
 
 		if (n.sourceCommit == null)
@@ -597,7 +626,7 @@ private boolean processOne(Candidate n) throws IOException {
 			// A 100% rename without any content change can also
 			// skip directly to the parent.
 			n.sourceCommit = parent;
-			n.sourcePath = PathFilter.create(r.getOldPath());
+			n.setSourcePath(PathFilter.create(r.getOldPath()));
 			push(n);
 			return false;
 		}
@@ -609,6 +638,21 @@ private boolean processOne(Candidate n) throws IOException {
 		return split(next, n);
 	}
 
+	private boolean blameEntireRegionOnParent(Candidate n, RevCommit parent) {
+		// File was not modified, blame parent.
+		n.sourceCommit = parent;
+		push(n);
+		return false;
+	}
+
+	private boolean splitBlameWithParent(Candidate n, RevCommit parent)
+			throws IOException {
+		Candidate next = n.create(parent, n.sourcePath);
+		next.sourceBlob = idBuf.toObjectId();
+		next.loadText(reader);
+		return split(next, n);
+	}
+
 	private boolean split(Candidate parent, Candidate source)
 			throws IOException {
 		EditList editList = diffAlgorithm.diff(textComparator,
@@ -636,26 +680,16 @@ private boolean split(Candidate parent, Candidate source)
 	private boolean processMerge(Candidate n) throws IOException {
 		int pCnt = n.getParentCount();
 
-		for (int pIdx = 0; pIdx < pCnt; pIdx++) {
-			RevCommit parent = n.getParent(pIdx);
-			if (parent.has(SEEN))
-				continue;
-			revPool.parseHeaders(parent);
-		}
-
 		// If any single parent exactly matches the merge, follow only
 		// that one parent through history.
 		ObjectId[] ids = null;
 		for (int pIdx = 0; pIdx < pCnt; pIdx++) {
 			RevCommit parent = n.getParent(pIdx);
-			if (parent.has(SEEN))
-				continue;
+			revPool.parseHeaders(parent);
 			if (!find(parent, n.sourcePath))
 				continue;
 			if (!(n instanceof ReverseCandidate) && idBuf.equals(n.sourceBlob)) {
-				n.sourceCommit = parent;
-				push(n);
-				return false;
+				return blameEntireRegionOnParent(n, parent);
 			}
 			if (ids == null)
 				ids = new ObjectId[pCnt];
@@ -668,8 +702,6 @@ private boolean processMerge(Candidate n) throws IOException {
 			renames = new DiffEntry[pCnt];
 			for (int pIdx = 0; pIdx < pCnt; pIdx++) {
 				RevCommit parent = n.getParent(pIdx);
-				if (parent.has(SEEN))
-					continue;
 				if (ids != null && ids[pIdx] != null)
 					continue;
 
@@ -689,7 +721,7 @@ private boolean processMerge(Candidate n) throws IOException {
 					// we choose to follow the one parent over trying to do
 					// possibly both parents.
 					n.sourceCommit = parent;
-					n.sourcePath = PathFilter.create(r.getOldPath());
+					n.setSourcePath(PathFilter.create(r.getOldPath()));
 					push(n);
 					return false;
 				}
@@ -702,8 +734,6 @@ private boolean processMerge(Candidate n) throws IOException {
 		Candidate[] parents = new Candidate[pCnt];
 		for (int pIdx = 0; pIdx < pCnt; pIdx++) {
 			RevCommit parent = n.getParent(pIdx);
-			if (parent.has(SEEN))
-				continue;
 
 			Candidate p;
 			if (renames != null && renames[pIdx] != null) {
@@ -927,20 +957,17 @@ public void release() {
 	private boolean find(RevCommit commit, PathFilter path) throws IOException {
 		treeWalk.setFilter(path);
 		treeWalk.reset(commit.getTree());
-		while (treeWalk.next()) {
-			if (path.isDone(treeWalk)) {
-				if (treeWalk.getFileMode(0).getObjectType() != OBJ_BLOB)
-					return false;
-				treeWalk.getObjectId(idBuf, 0);
-				return true;
-			}
-
-			if (treeWalk.isSubtree())
-				treeWalk.enterSubtree();
+		if (treeWalk.next() && isFile(treeWalk.getRawMode(0))) {
+			treeWalk.getObjectId(idBuf, 0);
+			return true;
 		}
 		return false;
 	}
 
+	private static final boolean isFile(int rawMode) {
+		return (rawMode & TYPE_FILE) == TYPE_FILE;
+	}
+
 	private DiffEntry findRename(RevCommit parent, RevCommit commit,
 			PathFilter path) throws IOException {
 		if (renameDetector == null)
@@ -961,4 +988,26 @@ private static boolean isRename(DiffEntry ent) {
 		return ent.getChangeType() == ChangeType.RENAME
 				|| ent.getChangeType() == ChangeType.COPY;
 	}
+
+	private static final TreeFilter ID_DIFF = new TreeFilter() {
+		@Override
+		public boolean include(TreeWalk tw) {
+			return !tw.idEqual(0, 1);
+		}
+
+		@Override
+		public boolean shouldBeRecursive() {
+			return false;
+		}
+
+		@Override
+		public TreeFilter clone() {
+			return this;
+		}
+
+		@Override
+		public String toString() {
+			return "ID_DIFF"; //$NON-NLS-1$
+		}
+	};
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/blame/Candidate.java b/org.eclipse.jgit/src/org/eclipse/jgit/blame/Candidate.java
index 95b4cec02..a652278d0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/blame/Candidate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/blame/Candidate.java
@@ -80,6 +80,7 @@ class Candidate {
 
 	/** Path of the candidate file in {@link #sourceCommit}. */
 	PathFilter sourcePath;
+	boolean recursivePath;
 
 	/** Unique name of the candidate blob in {@link #sourceCommit}. */
 	ObjectId sourceBlob;
@@ -110,6 +111,7 @@ class Candidate {
 	Candidate(RevCommit commit, PathFilter path) {
 		sourceCommit = commit;
 		sourcePath = path;
+		recursivePath = path.shouldBeRecursive();
 	}
 
 	int getParentCount() {
@@ -124,10 +126,18 @@ Candidate getNextCandidate(@SuppressWarnings("unused") int idx) {
 		return null;
 	}
 
+	boolean has(RevFlag flag) {
+		return sourceCommit.has(flag);
+	}
+
 	void add(RevFlag flag) {
 		sourceCommit.add(flag);
 	}
 
+	void remove(RevFlag flag) {
+		sourceCommit.remove(flag);
+	}
+
 	int getTime() {
 		return sourceCommit.getCommitTime();
 	}
@@ -136,6 +146,11 @@ PersonIdent getAuthor() {
 		return sourceCommit.getAuthorIdent();
 	}
 
+	void setSourcePath(PathFilter path) {
+		sourcePath = path;
+		recursivePath = path.shouldBeRecursive();
+	}
+
 	Candidate create(RevCommit commit, PathFilter path) {
 		return new Candidate(commit, path);
 	}
@@ -275,6 +290,42 @@ private Region clearRegionList() {
 		return r;
 	}
 
+	boolean canMergeRegions(Candidate other) {
+		return sourceCommit == other.sourceCommit
+				&& sourcePath.getPath().equals(other.sourcePath.getPath());
+	}
+
+	void mergeRegions(Candidate other) {
+		// regionList is always sorted by resultStart. Merge join two
+		// linked lists, preserving the ordering. Combine neighboring
+		// regions to reduce the number of results seen by callers.
+		Region a = clearRegionList();
+		Region b = other.clearRegionList();
+		Region t = null;
+
+		while (a != null && b != null) {
+			if (a.resultStart < b.resultStart) {
+				Region n = a.next;
+				t = add(t, this, a);
+				a = n;
+			} else {
+				Region n = b.next;
+				t = add(t, this, b);
+				b = n;
+			}
+		}
+
+		if (a != null) {
+			Region n = a.next;
+			t = add(t, this, a);
+			t.next = n;
+		} else /* b != null */{
+			Region n = b.next;
+			t = add(t, this, b);
+			t.next = n;
+		}
+	}
+
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
@@ -369,11 +420,22 @@ Candidate getNextCandidate(int idx) {
 			return parent;
 		}
 
+		@Override
+		boolean has(RevFlag flag) {
+			return true; // Pretend flag was added; sourceCommit is null.
+		}
+
 		@Override
 		void add(RevFlag flag) {
 			// Do nothing, sourceCommit is null.
 		}
 
+		@Override
+
+		void remove(RevFlag flag) {
+			// Do nothing, sourceCommit is null.
+		}
+
 		@Override
 		int getTime() {
 			return Integer.MAX_VALUE;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffAlgorithm.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffAlgorithm.java
index 7545821d1..39421c6de 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffAlgorithm.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffAlgorithm.java
@@ -114,6 +114,9 @@ public <S extends Sequence> EditList diff(
 			return EditList.singleton(region);
 
 		case REPLACE: {
+			if (region.getLengthA() == 1 && region.getLengthB() == 1)
+				return EditList.singleton(region);
+
 			SubsequenceComparator<S> cs = new SubsequenceComparator<S>(cmp);
 			Subsequence<S> as = Subsequence.a(a, region);
 			Subsequence<S> bs = Subsequence.b(b, region);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiff.java b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiff.java
index 026e63fce..0979db1e7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/diff/HistogramDiff.java
@@ -192,7 +192,10 @@ private void diff(Edit r) {
 				break;
 
 			case REPLACE:
-				diffReplace(r);
+				if (r.getLengthA() == 1 && r.getLengthB() == 1)
+					edits.add(r);
+				else
+					diffReplace(r);
 				break;
 
 			case EMPTY: