diff --git a/graphify/extract.py b/graphify/extract.py
index 03db9945..bfdaba7c 100644
--- a/graphify/extract.py
+++ b/graphify/extract.py
@@ -10,7 +10,7 @@ import sys
 import textwrap
 from collections import Counter
 from dataclasses import dataclass, field
-from pathlib import Path
+from pathlib import Path, PurePath
 from typing import Any, Callable
 
 from .cache import load_cached, save_cached
@@ -6574,6 +6574,31 @@ def extract(
     for e in all_edges:
         e["_origin"] = "ast"
 
+    # Canonicalize source_file to POSIX on every node AND edge (#2625).
+    #
+    # Extractors build source_file from the Path they were handed, so a run
+    # given RELATIVE inputs keeps the native separator on Windows. Only the
+    # relativizing branch of _sf_entry above ever calls as_posix(), so a single
+    # extraction could emit `src\lib\content.ts` and `src/pages/index.astro`
+    # side by side. source_file is compared as a STRING downstream
+    # (build._norm_source_file keying, _derive_prune_root, dedup, and
+    # analyze.find_import_cycles, which matches an edge's source_file against a
+    # node's by equality), so two spellings are two different files — the
+    # fragmentation of #683, and the reason the CLI path (which passes an
+    # explicit root) looked correct while the library entry point did not.
+    #
+    # Safe as a final pass: ids are minted through make_id, which collapses
+    # every non-word character — `\` and `/` alike — to `_`, so canonicalizing
+    # the separator here cannot desync an id from its source_file.
+    #
+    # PurePath is the NATIVE flavour on purpose: on POSIX a backslash is a legal
+    # filename character and must be left alone, so this only rewrites paths on
+    # the platform where `\` is actually a separator.
+    for _item in (*all_nodes, *all_edges):
+        _sf = _item.get("source_file")
+        if _sf and "\\" in str(_sf):
+            _item["source_file"] = PurePath(_sf).as_posix()
+
     return {
         "nodes": all_nodes,
         "edges": all_edges,
diff --git a/tests/test_extract.py b/tests/test_extract.py
index 693c1a25..8dc7a027 100644
--- a/tests/test_extract.py
+++ b/tests/test_extract.py
@@ -3328,3 +3328,54 @@ def test_rewire_does_not_bind_supertype_stub_to_function():
               "source_file": "store.py", "weight": 1.0}]
     _rewire_unique_stub_nodes(nodes, edges)
     assert edges[0]["target"] == "BookStore"  # inherits stub not bound to function
+
+
+def test_extract_emits_posix_source_file_for_relative_inputs(tmp_path):
+    r"""source_file must be canonical POSIX on every node AND edge, whatever
+    separator the caller's input paths used.
+
+    Extractors build source_file from the Path handed to them, and only the
+    relativizing branch of extract()'s remap calls as_posix(), so a run given
+    relative inputs used to keep the native separator on Windows — mixing
+    `src\lib\content.ts` and `src/pages/index.astro` in one extraction.
+    source_file is compared as a string downstream (build keying, prune-root
+    derivation, dedup, analyze.find_import_cycles), so two spellings are two
+    different files (#683 / #2625).
+
+    Uses the relative-input form deliberately: passing an explicit ``root``
+    takes the branch that already normalized, and would make this vacuous.
+    """
+    (tmp_path / "src" / "lib").mkdir(parents=True)
+    (tmp_path / "src" / "pages").mkdir(parents=True)
+    (tmp_path / "src" / "lib" / "content.ts").write_text(
+        "export function getPosts() { return []; }\n", encoding="utf-8"
+    )
+    (tmp_path / "src" / "pages" / "index.astro").write_text(
+        "---\nimport { getPosts } from '../lib/content';\n"
+        "const posts = getPosts();\n---\n<h1>{posts.length}</h1>\n",
+        encoding="utf-8",
+    )
+
+    cwd = os.getcwd()
+    os.chdir(tmp_path)
+    try:
+        result = extract([Path("src/lib/content.ts"), Path("src/pages/index.astro")])
+    finally:
+        os.chdir(cwd)
+
+    carriers = [
+        (kind, item.get("source_file"))
+        for kind, items in (("node", result["nodes"]), ("edge", result["edges"]))
+        for item in items
+        if item.get("source_file")
+    ]
+    assert carriers, "fixture produced nothing with a source_file; test would be vacuous"
+
+    offenders = [(kind, sf) for kind, sf in carriers if "\\" in sf]
+    assert not offenders, f"native separator survived into source_file: {offenders}"
+
+    # ...and both files are present under one spelling each, so the graph sees
+    # two files rather than four.
+    assert {sf for _, sf in carriers} == {
+        "src/lib/content.ts", "src/pages/index.astro",
+    }
diff --git a/tests/test_js_import_resolution.py b/tests/test_js_import_resolution.py
index 49452a98..d62c4458 100644
--- a/tests/test_js_import_resolution.py
+++ b/tests/test_js_import_resolution.py
@@ -1407,8 +1407,11 @@ def test_alias_import_does_not_remap_an_owned_symbol_id(tmp_path, monkeypatch):
     }
     target_symbol = _make_id(_file_stem(target), "formatDate")
     mirror_symbol = _make_id(_file_stem(mirror), "formatDate")
-    assert symbols[str(target)] == target_symbol
-    assert symbols[str(mirror)] == mirror_symbol
+    # as_posix, not str: source_file is canonical POSIX in extract() output
+    # (#2625), while str(Path(...)) is the native spelling and so only matched
+    # on POSIX hosts.
+    assert symbols[target.as_posix()] == target_symbol
+    assert symbols[mirror.as_posix()] == mirror_symbol
 
     imports = [
         edge
@@ -1418,8 +1421,8 @@ def test_alias_import_does_not_remap_an_owned_symbol_id(tmp_path, monkeypatch):
     by_source: dict[str, list[str]] = {}
     for edge in imports:
         by_source.setdefault(edge["source_file"], []).append(edge["target"])
-    assert by_source[str(button)] == [target_symbol]
-    assert by_source[str(mirror_user)] == [mirror_symbol]
+    assert by_source[button.as_posix()] == [target_symbol]
+    assert by_source[mirror_user.as_posix()] == [mirror_symbol]
     assert all(edge["source"] in node_ids and edge["target"] in node_ids for edge in imports)