diff --git a/graphify/extractors/markdown.py b/graphify/extractors/markdown.py
index d6d45ac8f..e3c19a797 100644
--- a/graphify/extractors/markdown.py
+++ b/graphify/extractors/markdown.py
@@ -133,7 +133,7 @@ def add_link(raw: str, line: int) -> None:
         # Skip over fenced code blocks so their contents are not parsed as
         # headings, but do not emit nodes/edges for them (#1077).
         stripped = line_text.strip()
-        if stripped.startswith("```"):
+        if stripped.startswith(("```", "~~~")):
             in_code_block = not in_code_block
             continue
 
diff --git a/tests/test_languages.py b/tests/test_languages.py
index f36ea7603..a3816c1db 100644
--- a/tests/test_languages.py
+++ b/tests/test_languages.py
@@ -2239,6 +2239,22 @@ def test_markdown_fenced_heading_not_parsed():
     assert not any("Not A Heading" in l for l in labels), \
         f"fenced '## Not A Heading' was incorrectly parsed as a node: {labels}"
 
+
+def test_markdown_tilde_fenced_heading_not_parsed(tmp_path):
+    path = tmp_path / "tilde-fenced-heading.md"
+    path.write_text(
+        "# Real Heading\n\n"
+        "~~~python\n"
+        "# Not A Heading\n"
+        "~~~\n"
+    )
+
+    r = extract_markdown(path)
+    labels = _labels(r)
+
+    assert any("Real Heading" in label for label in labels)
+    assert not any("Not A Heading" in label for label in labels)
+
 def test_markdown_no_dangling_edges():
     r = extract_markdown(FIXTURES / "deploy_guide.md")
     node_ids = {n["id"] for n in r["nodes"]}
@@ -2290,6 +2306,21 @@ def test_markdown_link_skips_external_and_images(tmp_path):
         assert "logo" not in e["target"]
 
 
+def test_markdown_tilde_fenced_link_not_parsed(tmp_path):
+    path = tmp_path / "tilde-fenced-link.md"
+    path.write_text(
+        "# Real Heading\n\n"
+        "~~~markdown\n"
+        "[Not A Reference](./hidden.md)\n"
+        "~~~\n"
+    )
+
+    r = extract_markdown(path)
+    refs = [e for e in r["edges"] if e["relation"] == "references"]
+
+    assert not refs
+
+
 def test_markdown_link_edges_resolve_to_real_nodes(tmp_path):
     """End-to-end: after extract()'s ID remap, link targets are real doc nodes,
     so the hub doc gains edges into existing nodes instead of ghost nodes (#1376)."""