diff --git a/hgext/rebase.py b/hgext/rebase.py
index 7bec3f697d76ea4c61ae99154a577fecd30fe15e_aGdleHQvcmViYXNlLnB5..ad9db007656f8acb369090f4a7b2a8785bcdef4f_aGdleHQvcmViYXNlLnB5 100644
--- a/hgext/rebase.py
+++ b/hgext/rebase.py
@@ -447,6 +447,10 @@
         repo.ui.debug(" already in target\n")
     repo.dirstate.write()
     repo.ui.debug(" merge against %d:%s\n" % (repo[rev].rev(), repo[rev]))
-    base = None
-    if repo[rev].rev() != repo[min(state)].rev():
+    if repo[rev].rev() == repo[min(state)].rev():
+        # Case (1) initial changeset of a non-detaching rebase.
+        # Let the merge mechanism find the base itself.
+        base = None
+    elif not repo[rev].p2():
+        # Case (2) detaching the node with a single parent, use this parent
         base = repo[rev].p1().node()
@@ -452,4 +456,35 @@
         base = repo[rev].p1().node()
+    else:
+        # In case of merge, we need to pick the right parent as merge base.
+        #
+        # Imagine we have:
+        # - M: currently rebase revision in this step
+        # - A: one parent of M
+        # - B: second parent of M
+        # - D: destination of this merge step (p1 var)
+        #
+        # If we are rebasing on D, D is the successors of A or B. The right
+        # merge base is the one D succeed to. We pretend it is B for the rest
+        # of this comment
+        #
+        # If we pick B as the base, the merge involves:
+        # - changes from B to M (actual changeset payload)
+        # - changes from B to D (induced by rebase) as D is a rebased
+        #   version of B)
+        # Which exactly represent the rebase operation.
+        #
+        # If we pick the A as the base, the merge involves
+        # - changes from A to M (actual changeset payload)
+        # - changes from A to D (with include changes between unrelated A and B
+        #   plus changes induced by rebase)
+        # Which does not represent anything sensible and creates a lot of
+        # conflicts.
+        for p in repo[rev].parents():
+            if state.get(p.rev()) == repo[p1].rev():
+                base = p.node()
+                break
+    if base is not None:
+        repo.ui.debug("   detach base %d:%s\n" % (repo[base].rev(), repo[base]))
     # When collapsing in-place, the parent is the common ancestor, we
     # have to allow merging with it.
     return merge.update(repo, rev, True, True, False, base, collapse)
diff --git a/tests/bundles/issue4041.hg b/tests/bundles/issue4041.hg
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diff --git a/tests/test-rebase-conflicts.t b/tests/test-rebase-conflicts.t
index 7bec3f697d76ea4c61ae99154a577fecd30fe15e_dGVzdHMvdGVzdC1yZWJhc2UtY29uZmxpY3RzLnQ=..ad9db007656f8acb369090f4a7b2a8785bcdef4f_dGVzdHMvdGVzdC1yZWJhc2UtY29uZmxpY3RzLnQ= 100644
--- a/tests/test-rebase-conflicts.t
+++ b/tests/test-rebase-conflicts.t
@@ -124,3 +124,184 @@
    * mybook                    5:d67b21408fc0
 
   $ cd ..
+
+Check that the right ancestors is used while rebasing a merge (issue4041)
+
+  $ hg clone "$TESTDIR/bundles/issue4041.hg" issue4041
+  requesting all changes
+  adding changesets
+  adding manifests
+  adding file changes
+  added 11 changesets with 8 changes to 3 files (+1 heads)
+  updating to branch default
+  2 files updated, 0 files merged, 0 files removed, 0 files unresolved
+  $ cd issue4041
+  $ hg phase --draft --force 9
+  $ hg log -G
+  o    changeset:   10:2f2496ddf49d
+  |\   branch:      f1
+  | |  tag:         tip
+  | |  parent:      7:4c9fbe56a16f
+  | |  parent:      9:e31216eec445
+  | |  user:        szhang
+  | |  date:        Thu Sep 05 12:59:39 2013 -0400
+  | |  summary:     merge
+  | |
+  | o  changeset:   9:e31216eec445
+  | |  branch:      f1
+  | |  user:        szhang
+  | |  date:        Thu Sep 05 12:59:10 2013 -0400
+  | |  summary:     more changes to f1
+  | |
+  | o    changeset:   8:8e4e2c1a07ae
+  | |\   branch:      f1
+  | | |  parent:      2:4bc80088dc6b
+  | | |  parent:      6:400110238667
+  | | |  user:        szhang
+  | | |  date:        Thu Sep 05 12:57:59 2013 -0400
+  | | |  summary:     bad merge
+  | | |
+  o | |  changeset:   7:4c9fbe56a16f
+  |/ /   branch:      f1
+  | |    parent:      2:4bc80088dc6b
+  | |    user:        szhang
+  | |    date:        Thu Sep 05 12:54:00 2013 -0400
+  | |    summary:     changed f1
+  | |
+  | o  changeset:   6:400110238667
+  | |  branch:      f2
+  | |  parent:      4:12e8ec6bb010
+  | |  user:        szhang
+  | |  date:        Tue Sep 03 13:58:02 2013 -0400
+  | |  summary:     changed f2 on f2
+  | |
+  | | @  changeset:   5:d79e2059b5c0
+  | | |  parent:      3:8a951942e016
+  | | |  user:        szhang
+  | | |  date:        Tue Sep 03 13:57:39 2013 -0400
+  | | |  summary:     changed f2 on default
+  | | |
+  | o |  changeset:   4:12e8ec6bb010
+  | |/   branch:      f2
+  | |    user:        szhang
+  | |    date:        Tue Sep 03 13:57:18 2013 -0400
+  | |    summary:     created f2 branch
+  | |
+  | o  changeset:   3:8a951942e016
+  | |  parent:      0:24797d4f68de
+  | |  user:        szhang
+  | |  date:        Tue Sep 03 13:57:11 2013 -0400
+  | |  summary:     added f2.txt
+  | |
+  o |  changeset:   2:4bc80088dc6b
+  | |  branch:      f1
+  | |  user:        szhang
+  | |  date:        Tue Sep 03 13:56:20 2013 -0400
+  | |  summary:     added f1.txt
+  | |
+  o |  changeset:   1:ef53c9e6b608
+  |/   branch:      f1
+  |    user:        szhang
+  |    date:        Tue Sep 03 13:55:26 2013 -0400
+  |    summary:     created f1 branch
+  |
+  o  changeset:   0:24797d4f68de
+     user:        szhang
+     date:        Tue Sep 03 13:55:08 2013 -0400
+     summary:     added default.txt
+  
+  $ hg rebase -s9 -d2 --debug # use debug to really check merge base used
+  rebase onto 2 starting from [<changectx e31216eec445>]
+  rebasing: 9:e31216eec445 5/6 changesets (83.33%)
+   future parents are 2 and -1
+  rebase status stored
+   update to 2:4bc80088dc6b
+  resolving manifests
+   branchmerge: False, force: True, partial: False
+   ancestor: d79e2059b5c0+, local: d79e2059b5c0+, remote: 4bc80088dc6b
+   f2.txt: other deleted -> r
+   f1.txt: remote created -> g
+  removing f2.txt
+  updating: f2.txt 1/2 files (50.00%)
+  getting f1.txt
+  updating: f1.txt 2/2 files (100.00%)
+   merge against 9:e31216eec445
+     detach base 8:8e4e2c1a07ae
+    searching for copies back to rev 3
+  resolving manifests
+   branchmerge: True, force: True, partial: False
+   ancestor: 8e4e2c1a07ae, local: 4bc80088dc6b+, remote: e31216eec445
+   f1.txt: remote is newer -> g
+  getting f1.txt
+  updating: f1.txt 1/1 files (100.00%)
+  f1.txt
+  rebasing: 10:2f2496ddf49d 6/6 changesets (100.00%)
+   future parents are 11 and 7
+  rebase status stored
+   already in target
+   merge against 10:2f2496ddf49d
+     detach base 9:e31216eec445
+    searching for copies back to rev 3
+  resolving manifests
+   branchmerge: True, force: True, partial: False
+   ancestor: e31216eec445, local: 19c888675e13+, remote: 2f2496ddf49d
+   f1.txt: remote is newer -> g
+  getting f1.txt
+  updating: f1.txt 1/1 files (100.00%)
+  f1.txt
+  rebase merging completed
+  update back to initial working directory parent
+  resolving manifests
+   branchmerge: False, force: False, partial: False
+   ancestor: 2a7f09cac94c, local: 2a7f09cac94c+, remote: d79e2059b5c0
+   f1.txt: other deleted -> r
+   f2.txt: remote created -> g
+  removing f1.txt
+  updating: f1.txt 1/2 files (50.00%)
+  getting f2.txt
+  updating: f2.txt 2/2 files (100.00%)
+  3 changesets found
+  list of changesets:
+  4c9fbe56a16f30c0d5dcc40ec1a97bbe3325209c
+  e31216eec445e44352c5f01588856059466a24c9
+  2f2496ddf49d69b5ef23ad8cf9fb2e0e4faf0ac2
+  bundling: 1/3 changesets (33.33%)
+  bundling: 2/3 changesets (66.67%)
+  bundling: 3/3 changesets (100.00%)
+  bundling: 1/3 manifests (33.33%)
+  bundling: 2/3 manifests (66.67%)
+  bundling: 3/3 manifests (100.00%)
+  bundling: f1.txt 1/1 files (100.00%)
+  saved backup bundle to $TESTTMP/issue4041/.hg/strip-backup/e31216eec445-backup.hg (glob)
+  3 changesets found
+  list of changesets:
+  4c9fbe56a16f30c0d5dcc40ec1a97bbe3325209c
+  19c888675e133ab5dff84516926a65672eaf04d9
+  2a7f09cac94c7f4b73ebd5cd1a62d3b2e8e336bf
+  bundling: 1/3 changesets (33.33%)
+  bundling: 2/3 changesets (66.67%)
+  bundling: 3/3 changesets (100.00%)
+  bundling: 1/3 manifests (33.33%)
+  bundling: 2/3 manifests (66.67%)
+  bundling: 3/3 manifests (100.00%)
+  bundling: f1.txt 1/1 files (100.00%)
+  adding branch
+  adding changesets
+  changesets: 1 chunks
+  add changeset 4c9fbe56a16f
+  changesets: 2 chunks
+  add changeset 19c888675e13
+  changesets: 3 chunks
+  add changeset 2a7f09cac94c
+  adding manifests
+  manifests: 1/2 chunks (50.00%)
+  manifests: 2/2 chunks (100.00%)
+  manifests: 3/2 chunks (150.00%)
+  adding file changes
+  adding f1.txt revisions
+  files: 1/1 chunks (100.00%)
+  added 2 changesets with 2 changes to 1 files
+  removing unknown node e31216eec445 from 1-phase boundary
+  invalid branchheads cache (served): tip differs
+  rebase completed
+  updating the branch cache