diff --git a/cogapp/cogapp.py b/cogapp/cogapp.py
index b463f87..ffa2470 100644
--- a/cogapp/cogapp.py
+++ b/cogapp/cogapp.py
@@ -125,6 +125,10 @@ def get_code(self):
         # If the markers and lines all have the same prefix
         # (end-of-line comment chars, for example),
         # then remove it from all the lines.
+        for idx, marker in enumerate(self.markers):
+            self.markers[idx] = marker.replace(self.options.begin_spec, "").replace(
+                self.options.end_spec, ""
+            )
         pref_in = common_prefix(self.markers + self.lines)
         if pref_in:
             self.markers = [line.replace(pref_in, "", 1) for line in self.markers]
diff --git a/cogapp/test_cogapp.py b/cogapp/test_cogapp.py
index 1ab7969..783d827 100644
--- a/cogapp/test_cogapp.py
+++ b/cogapp/test_cogapp.py
@@ -254,6 +254,30 @@ def test_prefixed_indented_code(self):
         infile = reindent_block(infile)
         self.assertEqual(Cog().process_string(infile), infile)
 
+    def test_markers_overlapping_prefix(self):
+        infile = """\
+            // cog-begin
+            // cog.outl('lorem ipsum')
+            // cog-middle
+            // cog-end
+            """
+
+        outfile = """\
+            // cog-begin
+            // cog.outl('lorem ipsum')
+            // cog-middle
+            lorem ipsum
+            // cog-end
+            """
+
+        infile = reindent_block(infile)
+        outfile = reindent_block(outfile)
+        cog = Cog()
+        cog.options.begin_spec = "cog-begin"
+        cog.options.end_spec = "cog-middle"
+        cog.options.end_output = "cog-end"
+        self.assertEqual(cog.process_string(infile), outfile)
+
     def test_bogus_prefix_match(self):
         infile = """\
             prologue