diff --git a/Doc/distutils/sourcedist.rst b/Doc/distutils/sourcedist.rst
--- a/Doc/distutils/sourcedist.rst
+++ b/Doc/distutils/sourcedist.rst
@@ -103,6 +103,10 @@ per line, regular files (or symlinks to 
 :file:`MANIFEST`, you must specify everything: the default set of files
 described above does not apply in this case.
 
+.. versionadded:: 3.2
+   :file:`MANIFEST` files start with a comment indicated they are generated.
+   Files without this comment are not overwritten or removed.
+
 The manifest template has one command per line, where each command specifies a
 set of files to include or exclude from the source distribution.  For an
 example, again we turn to the Distutils' own manifest template::
diff --git a/Lib/distutils/command/sdist.py b/Lib/distutils/command/sdist.py
--- a/Lib/distutils/command/sdist.py
+++ b/Lib/distutils/command/sdist.py
@@ -335,8 +335,21 @@ class sdist(Command):
         by 'add_defaults()' and 'read_template()') to the manifest file
         named by 'self.manifest'.
         """
-        self.execute(file_util.write_file,
-                     (self.manifest, self.filelist.files),
+        if os.path.isfile(self.manifest):
+            fp = open(self.manifest)
+            try:
+                first_line = fp.readline()
+            finally:
+                fp.close()
+
+            if first_line != '# file GENERATED by distutils, do NOT edit\n':
+                log.info("not writing to manually maintained "
+                         "manifest file '%s'" % self.manifest)
+                return
+
+        content = self.filelist.files[:]
+        content.insert(0, '# file GENERATED by distutils, do NOT edit')
+        self.execute(file_util.write_file, (self.manifest, content),
                      "writing manifest file '%s'" % self.manifest)
 
     def read_manifest(self):
diff --git a/Lib/distutils/tests/test_sdist.py b/Lib/distutils/tests/test_sdist.py
--- a/Lib/distutils/tests/test_sdist.py
+++ b/Lib/distutils/tests/test_sdist.py
@@ -29,6 +29,7 @@ setup(name='fake')
 """
 
 MANIFEST = """\
+# file GENERATED by distutils, do NOT edit
 README
 inroot.txt
 setup.py
@@ -294,7 +295,7 @@ class SDistTestCase(PyPIRCCommandTestCas
         finally:
             f.close()
 
-        self.assertEquals(len(manifest), 4)
+        self.assertEquals(len(manifest), 5)
 
         # adding a file
         self.write_file((self.tmp_dir, 'somecode', 'doc2.txt'), '#')
@@ -314,9 +315,40 @@ class SDistTestCase(PyPIRCCommandTestCas
             f.close()
 
         # do we have the new file in MANIFEST ?
-        self.assertEquals(len(manifest2), 5)
+        self.assertEquals(len(manifest2), 6)
         self.assertIn('doc2.txt', manifest2[-1])
 
+    def test_manifest_marker(self):
+        # check that autogenerated MANIFESTs have a marker
+        dist, cmd = self.get_cmd()
+        cmd.ensure_finalized()
+        cmd.run()
+
+        f = open(cmd.manifest)
+        try:
+            manifest = [line.strip() for line in f.read().split('\n')
+                        if line.strip() != '']
+        finally:
+            f.close()
+
+        self.assertEqual(manifest[0],
+                         '# file GENERATED by distutils, do NOT edit')
+
+    def test_manual_manifest(self):
+        # check that a MANIFEST without a marker is left alone
+        dist, cmd = self.get_cmd()
+        cmd.ensure_finalized()
+        self.write_file((self.tmp_dir, cmd.manifest), 'README.manual')
+        cmd.run()
+
+        f = open(cmd.manifest)
+        try:
+            manifest = [line.strip() for line in f.read().split('\n')
+                        if line.strip() != '']
+        finally:
+            f.close()
+
+        self.assertEqual(manifest, ['README.manual'])
 
 def test_suite():
     return unittest.makeSuite(SDistTestCase)
diff --git a/Misc/NEWS b/Misc/NEWS
--- a/Misc/NEWS
+++ b/Misc/NEWS
@@ -83,6 +83,10 @@ Extensions
 Library
 -------
 
+- Issue #8688: MANIFEST files created by distutils now include a magic
+  comment indicating they are generated. Manually maintained MANIFESTs
+  without this marker will not be overwritten or removed.
+
 - Issue #7467: when reading a file from a ZIP archive, its CRC is checked
   and a BadZipfile error is raised if it doesn't match (as used to be the
   case in Python 2.5 and earlier).