diff --git a/incorporealcms/markdown.py b/incorporealcms/markdown.py
index 3999457..8a36784 100644
--- a/incorporealcms/markdown.py
+++ b/incorporealcms/markdown.py
@@ -58,7 +58,18 @@ def parse_md(path: str, pages_root: str):
         with open(absolute_path, 'r') as input_file:
             mtime = datetime.datetime.fromtimestamp(os.path.getmtime(input_file.name), tz=datetime.timezone.utc)
             entry = input_file.read()
+
         logger.debug("path '%s' read", absolute_path)
+
+        # remove .md extensions used for navigating in vim and replace them with
+        # the pattern we use for HTML output here
+        # foo/index.md -> foo/, foo/index.md#anchor -> foo/#anchor
+        # ../index.md -> ../, ../index.md#anchor -> ../#anchor
+        entry = re.sub(r'\[([^]]+)\]\(([^)]+)index.md(#[^)]*)?\)', r'[\1](\2\3)', entry)
+        # index.md -> ., index.md#anchor -> .#anchor
+        entry = re.sub(r'\[([^]]+)\]\(index.md(#[^)]*)?\)', r'[\1](.\2)', entry)
+        # bar.md -> bar, foo/bar.md -> foo/bar, bar.md#anchor -> bar#anchor
+        entry = re.sub(r'\[([^]]+)\]\(([^)]+).md(#[^)]*)?\)', r'[\1](\2\3)', entry)
         md = init_md()
         content = Markup(md.convert(entry))     # nosec B704
     except (OSError, FileNotFoundError):
diff --git a/tests/instance/pages/file-with-index.md-link.md b/tests/instance/pages/file-with-index.md-link.md
new file mode 100644
index 0000000..6cfae0b
--- /dev/null
+++ b/tests/instance/pages/file-with-index.md-link.md
@@ -0,0 +1,6 @@
+[Cool](cool/index.md)
+[Anchored Cool](cool/index.md#anchor)
+[This Index](index.md)
+[Anchored This Index](index.md#anchor)
+[Parent](../index.md)
+[Anchored Parent](../index.md#anchor)
diff --git a/tests/instance/pages/file-with-md-link.md b/tests/instance/pages/file-with-md-link.md
new file mode 100644
index 0000000..b59d55b
--- /dev/null
+++ b/tests/instance/pages/file-with-md-link.md
@@ -0,0 +1,4 @@
+[Foo](foo.md)
+[Anchored Foo](foo.md#anchor)
+[Sub Foo](sub/foo.md)
+[Anchored Sub Foo](sub/foo.md#anchor)
diff --git a/tests/test_markdown.py b/tests/test_markdown.py
index 13c6312..71932a0 100644
--- a/tests/test_markdown.py
+++ b/tests/test_markdown.py
@@ -163,3 +163,23 @@ def test_parse_md_bad_file():
     """Test the direct results of parsing a markdown file."""
     with pytest.raises(ValueError):
         content, md, page_name, page_title, mtime = parse_md(os.path.join(PAGES_DIR, 'actually-a-png.md'), PAGES_DIR)
+
+
+def test_md_extension_in_source_link_is_stripped():
+    """Test that if a foo.md file link is specified in the Markdown, it is foo in the HTML."""
+    content, _, _, _, _ = parse_md(os.path.join(PAGES_DIR, 'file-with-md-link.md'), PAGES_DIR)
+    assert '<a href="foo">Foo</a>' in content
+    assert '<a href="foo#anchor">Anchored Foo</a>' in content
+    assert '<a href="sub/foo">Sub Foo</a>' in content
+    assert '<a href="sub/foo#anchor">Anchored Sub Foo</a>' in content
+
+
+def test_index_in_source_link_is_stripped():
+    """Test that if a index.md file link is specified in the Markdown, it is just the dir in the HTML."""
+    content, _, _, _, _ = parse_md(os.path.join(PAGES_DIR, 'file-with-index.md-link.md'), PAGES_DIR)
+    assert '<a href="cool/">Cool</a>' in content
+    assert '<a href="cool/#anchor">Anchored Cool</a>' in content
+    assert '<a href=".">This Index</a>' in content
+    assert '<a href=".#anchor">Anchored This Index</a>' in content
+    assert '<a href="../">Parent</a>' in content
+    assert '<a href="../#anchor">Anchored Parent</a>' in content