diff --git a/Utility/SshConfig.hs b/Utility/SshConfig.hs
index ca336a4b8d..57e4f0f389 100644
--- a/Utility/SshConfig.hs
+++ b/Utility/SshConfig.hs
@@ -15,6 +15,7 @@ import Utility.FileMode
 import Data.Char
 import Data.Ord
 import Data.Either
+import System.Directory
 
 data SshConfig
 	= GlobalConfig SshSetting
@@ -117,8 +118,11 @@ changeUserSshConfig modifier = do
 	whenM (doesFileExist configfile) $ do
 		c <- readFileStrict configfile
 		let c' = modifier c
-		when (c /= c') $
-			viaTmp writeSshConfig configfile c'
+		when (c /= c') $ do
+			-- If it's a symlink, replace the file it
+			-- points to.
+			f <- catchDefaultIO configfile (canonicalizePath configfile)
+			viaTmp writeSshConfig f c'
 
 writeSshConfig :: FilePath -> String -> IO ()
 writeSshConfig f s = do
diff --git a/debian/changelog b/debian/changelog
index 0ded62f123..e13e648e40 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ git-annex (5.20150917) UNRELEASED; urgency=medium
 
   * info: Don't allow use in a non-git-annex repository, since it
     uses the git-annex branch and would create it if it were missing.
+  * assistant: When updating ~/.ssh/config, preserve any symlinks.
 
  -- Joey Hess <id@joeyh.name>  Wed, 16 Sep 2015 12:23:33 -0400
 
diff --git a/doc/bugs/git-annex_rewrites_.ssh__47__config/comment_1_030209c8c309e976761825c6c51a602d._comment b/doc/bugs/git-annex_rewrites_.ssh__47__config/comment_1_030209c8c309e976761825c6c51a602d._comment
new file mode 100644
index 0000000000..26df1211aa
--- /dev/null
+++ b/doc/bugs/git-annex_rewrites_.ssh__47__config/comment_1_030209c8c309e976761825c6c51a602d._comment
@@ -0,0 +1,15 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 1"""
+ date="2015-09-21T16:14:03Z"
+ content="""
+The assistant does not normally do this when you merely start it up. It does it
+when you configure a ssh remote, when it needs to modify that file.
+It might also modify the file on startup if it detects a configuration that
+an old version of the assistant put in that needs to be fixed up.
+
+Is the trailing whitespace you speak of just a newline added after the
+existing host block, or something else? Your "..." is not very clear.
+
+Fixed symlink issue in git.
+"""]]