diff --git a/mercurial/context.py b/mercurial/context.py
--- a/mercurial/context.py
+++ b/mercurial/context.py
@@ -1121,7 +1121,8 @@ class basefilectx(object):
                 hist[f] = curr
                 del pcache[f]
 
-        return pycompat.ziplist(hist[base][0], hist[base][1].splitlines(True))
+        lineattrs, text = hist[base]
+        return pycompat.ziplist(lineattrs, mdiff.splitnewlines(text))
 
     def ancestors(self, followfirst=False):
         visit = {}
diff --git a/tests/test-annotate.t b/tests/test-annotate.t
--- a/tests/test-annotate.t
+++ b/tests/test-annotate.t
@@ -895,6 +895,38 @@ Annotate with --ignore-blank-lines (simi
 
   $ cd ..
 
+Annotate with orphaned CR (issue5798)
+-------------------------------------
+
+  $ hg init repo-cr
+  $ cd repo-cr
+
+  $ substcr() {
+  > sed 's/\r/[CR]/g'
+  > }
+
+  >>> with open('a', 'wb') as f:
+  ...     f.write(b'0a\r0b\r\n0c\r0d\r\n0e\n0f\n0g')
+  $ hg ci -qAm0
+  >>> with open('a', 'wb') as f:
+  ...     f.write(b'0a\r0b\r\n1c\r1d\r\n0e\n1f\n0g')
+  $ hg ci -m1
+
+  $ hg annotate -r0 a | substcr
+  0: 0a[CR]0b[CR]
+  0: 0c[CR]0d[CR]
+  0: 0e
+  0: 0f
+  0: 0g
+  $ hg annotate -r1 a | substcr
+  0: 0a[CR]0b[CR]
+  1: 1c[CR]1d[CR]
+  0: 0e
+  1: 1f
+  0: 0g
+
+  $ cd ..
+
 Annotate with linkrev pointing to another branch
 ------------------------------------------------