diff --git a/mercurial/localrepo.py b/mercurial/localrepo.py
--- a/mercurial/localrepo.py
+++ b/mercurial/localrepo.py
@@ -787,10 +787,14 @@ class localrepository(repo.repository):
 
             # check subrepos
             subs = []
+            removedsubs = set()
+            for p in wctx.parents():
+                removedsubs.update(s for s in p.substate if match(s))
             for s in wctx.substate:
+                removedsubs.discard(s)
                 if match(s) and wctx.sub(s).dirty():
                     subs.append(s)
-            if subs and '.hgsubstate' not in changes[0]:
+            if (subs or removedsubs) and '.hgsubstate' not in changes[0]:
                 changes[0].insert(0, '.hgsubstate')
 
             # make sure all explicit patterns are matched
@@ -830,7 +834,7 @@ class localrepository(repo.repository):
             edited = (text != cctx._text)
 
             # commit subs
-            if subs:
+            if subs or removedsubs:
                 state = wctx.substate.copy()
                 for s in subs:
                     self.ui.status(_('committing subrepository %s\n') % s)
diff --git a/tests/test-subrepo b/tests/test-subrepo
--- a/tests/test-subrepo
+++ b/tests/test-subrepo
@@ -162,6 +162,28 @@ hg up 5
 hg merge 4    # try to merge default into br again
 cd ..
 
+echo % test subrepo delete from .hgsubstate
+hg init testdelete
+mkdir testdelete/nested testdelete/nested2
+hg init testdelete/nested
+hg init testdelete/nested2
+echo test > testdelete/nested/foo
+echo test > testdelete/nested2/foo
+hg -R testdelete/nested add
+hg -R testdelete/nested2 add
+hg -R testdelete/nested ci -m test
+hg -R testdelete/nested2 ci -m test
+echo nested = nested > testdelete/.hgsub
+echo nested2 = nested2 >> testdelete/.hgsub
+hg -R testdelete add
+hg -R testdelete ci -m "nested 1 & 2 added"
+echo nested = nested > testdelete/.hgsub
+hg -R testdelete ci -m "nested 2 deleted"
+cat testdelete/.hgsubstate | sed "s:.* ::"
+hg -R testdelete remove testdelete/.hgsub
+hg -R testdelete ci -m ".hgsub deleted"
+cat testdelete/.hgsubstate
+
 echo % test repository cloning
 mkdir mercurial mercurial2
 hg init nested_absolute
diff --git a/tests/test-subrepo.out b/tests/test-subrepo.out
--- a/tests/test-subrepo.out
+++ b/tests/test-subrepo.out
@@ -247,6 +247,13 @@ committing subrepository s
 0 files updated, 0 files merged, 0 files removed, 0 files unresolved
 1 files updated, 0 files merged, 0 files removed, 0 files unresolved
 (branch merge, don't forget to commit)
+% test subrepo delete from .hgsubstate
+adding testdelete/nested/foo
+adding testdelete/nested2/foo
+adding testdelete/.hgsub
+committing subrepository nested2
+committing subrepository nested
+nested
 % test repository cloning
 adding nested_absolute/foo
 adding nested_relative/foo2