diff --git a/graphify/analyze.py b/graphify/analyze.py
index cb6c7648..ec1e61a9 100644
--- a/graphify/analyze.py
+++ b/graphify/analyze.py
@@ -64,11 +64,12 @@ def _is_file_node(G: nx.Graph, node_id: str) -> bool:
     label = attrs.get("label", "")
     if not label:
         return False
-    # File-level hub: label matches the actual source filename (not just any label ending in .py)
+    # File-level hub: label matches the actual source filename — bare basename OR
+    # the directory-qualified form the #2032 disambiguation pass may assign.
     source_file = attrs.get("source_file", "")
     if source_file:
-        from pathlib import Path as _Path
-        if label == _Path(source_file).name:
+        from graphify.build import _is_file_node_label
+        if _is_file_node_label(label, source_file):
             return True
     # Method stub: AST extractor labels methods as '.method_name()'
     if label.startswith(".") and label.endswith("()"):
diff --git a/graphify/build.py b/graphify/build.py
index 6ce5e42d..a03524d8 100644
--- a/graphify/build.py
+++ b/graphify/build.py
@@ -174,6 +174,59 @@ def _abs_identity(p: str | None, root: str | None = None) -> str | None:
         return pp.as_posix()
 
 
+def _is_file_node_label(label: "str | None", source_file: "str | None") -> bool:
+    """Whether *label* is a file node's label for *source_file* — the bare
+    basename, OR a directory-qualified suffix produced by the disambiguation pass
+    below (#2032). Used both to recognize file nodes when relabeling and by the
+    downstream file-node predicates (analyze/tree/serve)."""
+    if not label or not source_file:
+        return False
+    sf = str(source_file).replace("\\", "/")
+    lbl = str(label)
+    if lbl == sf.rsplit("/", 1)[-1]:
+        return True
+    return "/" in lbl and (sf == lbl or sf.endswith("/" + lbl))
+
+
+def _shortest_unique_suffix(sf: str, all_sfs: "set[str]") -> str:
+    """Shortest trailing path suffix (basename + k parent dirs) of *sf* that is
+    unique among *all_sfs*. `a/b/index.ts` vs `c/b/index.ts` -> `a/b/index.ts`;
+    `x/index.ts` vs `y/index.ts` -> `x/index.ts`. Derived from the path (never the
+    current label) so relabeling is idempotent across incremental rebuilds."""
+    parts = [p for p in sf.replace("\\", "/").split("/") if p]
+    others = [
+        [p for p in o.replace("\\", "/").split("/") if p]
+        for o in all_sfs if o != sf
+    ]
+    for k in range(1, len(parts) + 1):
+        suffix = parts[-k:]
+        if all(o[-k:] != suffix for o in others):
+            return "/".join(suffix)
+    return "/".join(parts)
+
+
+def _disambiguate_file_node_labels(G: "nx.Graph") -> None:
+    """Give file nodes that share a basename a directory-qualified label so
+    `explain`/discovery can tell them apart (#2032). Repos where every basename
+    is unique are untouched (labels stay bare). Ids/edges are never changed —
+    only display labels. Idempotent: labels derive from source_file, not the
+    current (possibly already-qualified) label."""
+    from collections import defaultdict
+    groups: dict[str, list[tuple[str, str]]] = defaultdict(list)
+    for nid, attrs in G.nodes(data=True):
+        sf = attrs.get("source_file")
+        label = attrs.get("label")
+        if sf and label and _is_file_node_label(str(label), str(sf)):
+            basename = str(sf).replace("\\", "/").rsplit("/", 1)[-1]
+            groups[basename].append((nid, str(sf)))
+    for members in groups.values():
+        distinct = {sf for _, sf in members}
+        if len(distinct) < 2:
+            continue  # no collision — leave the bare basename label
+        for nid, sf in members:
+            G.nodes[nid]["label"] = _shortest_unique_suffix(sf, distinct)
+
+
 def _infer_merge_root(graph_path: Path) -> str | None:
     """Best-effort scan root for relativizing paths in build_merge when the caller
     passes no ``root`` (#1571).
@@ -860,6 +913,11 @@ def build_from_json(extraction: dict, *, directed: bool = False, root: str | Pat
             kept_hyperedges.append(he)
         if kept_hyperedges:
             G.graph["hyperedges"] = kept_hyperedges
+    # Runs LAST, after the alias-competition above (which relies on file-node
+    # labels still being bare basenames): give colliding-basename file nodes a
+    # directory-qualified display label so lookup/discovery can disambiguate
+    # them (#2032). Labels only — ids and edges are untouched.
+    _disambiguate_file_node_labels(G)
     return G
 
 
diff --git a/graphify/serve.py b/graphify/serve.py
index 457171e5..eab34f39 100644
--- a/graphify/serve.py
+++ b/graphify/serve.py
@@ -947,13 +947,15 @@ def _find_node(G: nx.Graph, label: str) -> list[str]:
 
     if source_exact:
         query_basename = _strip_diacritics(Path(label).name).lower()
-        preferred = [
-            nid
-            for nid in source_exact
-            if str(G.nodes[nid].get("source_location", "")) == "L1"
-            and _strip_diacritics(str(G.nodes[nid].get("label") or "")).lower()
-            == query_basename
-        ]
+        preferred = []
+        for nid in source_exact:
+            if str(G.nodes[nid].get("source_location", "")) != "L1":
+                continue
+            # File-node label is the bare basename OR a directory-qualified form
+            # from the #2032 disambiguation pass (e.g. "process-order/index.ts").
+            lbl = _strip_diacritics(str(G.nodes[nid].get("label") or "")).lower()
+            if lbl == query_basename or lbl.endswith("/" + query_basename):
+                preferred.append(nid)
         if len(preferred) == 1:
             source_exact = preferred + [nid for nid in source_exact if nid != preferred[0]]
 
diff --git a/graphify/tree_html.py b/graphify/tree_html.py
index 94b10df4..1dc658ff 100644
--- a/graphify/tree_html.py
+++ b/graphify/tree_html.py
@@ -125,9 +125,12 @@ def build_tree(
         sym_children: List[Dict[str, Any]] = []
         for n in syms:
             label = n.get("label", n.get("id", "?"))
-            # Skip the redundant file-name node graphify emits.
-            if label == src_path.name and n.get("file_type") == "code":
-                continue
+            # Skip the redundant file-name node graphify emits (bare basename or
+            # the directory-qualified form from the #2032 disambiguation pass).
+            if n.get("file_type") == "code":
+                from graphify.build import _is_file_node_label
+                if _is_file_node_label(label, src_file):
+                    continue
             sym_children.append({
                 "name": label,
                 "total_count": 1,
diff --git a/tests/test_file_label_disambiguation.py b/tests/test_file_label_disambiguation.py
new file mode 100644
index 00000000..bc474fae
--- /dev/null
+++ b/tests/test_file_label_disambiguation.py
@@ -0,0 +1,109 @@
+"""File-node labels are disambiguated when basenames collide (#2032).
+
+In directory-per-entrypoint repos (Supabase Edge Functions, Next.js pages,
+Rust mod.rs, Python __init__.py) many files share a basename, so basename-only
+file-node labels collide and `explain`/discovery can't tell them apart. When a
+basename collides, file nodes get a shortest-unique directory-qualified label;
+unique basenames are left bare. Ids/edges are never changed — only labels.
+"""
+from __future__ import annotations
+
+import networkx as nx
+
+from graphify.build import (
+    _disambiguate_file_node_labels,
+    _is_file_node_label,
+    _shortest_unique_suffix,
+)
+
+
+def test_is_file_node_label_and_suffix_helpers():
+    assert _is_file_node_label("index.ts", "a/b/index.ts")
+    assert _is_file_node_label("b/index.ts", "a/b/index.ts")  # qualified form
+    assert not _is_file_node_label("index", "a/b/index.ts")   # a symbol, not the file
+    assert not _is_file_node_label("helper()", "a/b/index.ts")
+    all_sfs = {"supabase/functions/process-order/index.ts",
+               "supabase/functions/send-receipt/index.ts"}
+    assert _shortest_unique_suffix("supabase/functions/process-order/index.ts", all_sfs) == "process-order/index.ts"
+    # root-level file colliding with a nested one keeps the bare basename
+    assert _shortest_unique_suffix("index.ts", {"index.ts", "a/index.ts"}) == "index.ts"
+
+
+def _file_node(nid, sf):
+    return (nid, {"label": sf.rsplit("/", 1)[-1], "file_type": "code", "source_file": sf})
+
+
+def test_colliding_file_labels_are_qualified_uniques_left_bare():
+    G = nx.DiGraph()
+    for nid, sf in [
+        ("po", "supabase/functions/process-order/index.ts"),
+        ("sr", "supabase/functions/send-receipt/index.ts"),
+        ("main", "src/main.ts"),
+    ]:
+        G.add_node(nid, **_file_node(nid, sf)[1])
+    # a symbol inside one of the files must NOT be relabeled
+    G.add_node("sym", label="handler", file_type="code", source_file="supabase/functions/process-order/index.ts")
+
+    _disambiguate_file_node_labels(G)
+
+    assert G.nodes["po"]["label"] == "process-order/index.ts"
+    assert G.nodes["sr"]["label"] == "send-receipt/index.ts"
+    assert G.nodes["main"]["label"] == "main.ts", "unique basename must stay bare"
+    assert G.nodes["sym"]["label"] == "handler", "symbol nodes must be untouched"
+
+
+def test_disambiguation_is_idempotent():
+    G = nx.DiGraph()
+    G.add_node("a", label="index.ts", file_type="code", source_file="x/a/index.ts")
+    G.add_node("b", label="index.ts", file_type="code", source_file="x/b/index.ts")
+    _disambiguate_file_node_labels(G)
+    first = {n: G.nodes[n]["label"] for n in G}
+    # Re-run over already-qualified labels: must be stable (derived from path).
+    _disambiguate_file_node_labels(G)
+    assert {n: G.nodes[n]["label"] for n in G} == first
+    assert first == {"a": "a/index.ts", "b": "b/index.ts"}
+
+
+def test_three_way_collision_grows_suffix_until_unique():
+    G = nx.DiGraph()
+    G.add_node("a", label="index.ts", file_type="code", source_file="a/x/index.ts")
+    G.add_node("b", label="index.ts", file_type="code", source_file="b/x/index.ts")
+    _disambiguate_file_node_labels(G)
+    # basename + one dir ("x/index.ts") still collides, so grow to two dirs.
+    assert G.nodes["a"]["label"] == "a/x/index.ts"
+    assert G.nodes["b"]["label"] == "b/x/index.ts"
+
+
+def test_end_to_end_build_and_lookup(tmp_path):
+    """Full pipeline: two entry-point index.ts files get distinguishable labels
+    and both resolve via serve._find_node."""
+    from graphify.extract import extract
+    from graphify.build import build_from_json
+    from graphify.serve import _find_node
+
+    fns = tmp_path / "supabase" / "functions"
+    (fns / "process-order").mkdir(parents=True)
+    (fns / "send-receipt").mkdir(parents=True)
+    (fns / "process-order" / "index.ts").write_text("export function processOrder() { return 1; }\n")
+    (fns / "send-receipt" / "index.ts").write_text("export function sendReceipt() { return 2; }\n")
+    (tmp_path / "main.ts").write_text("export function main() { return 0; }\n")
+
+    result = extract(
+        [fns / "process-order" / "index.ts", fns / "send-receipt" / "index.ts", tmp_path / "main.ts"],
+        cache_root=tmp_path / "cache", parallel=False,
+    )
+    G = build_from_json(result, root=str(tmp_path))
+
+    file_labels = {
+        d["label"] for _, d in G.nodes(data=True)
+        if _is_file_node_label(d.get("label"), d.get("source_file"))
+    }
+    assert "process-order/index.ts" in file_labels
+    assert "send-receipt/index.ts" in file_labels
+    assert "main.ts" in file_labels  # unique basename stays bare
+
+    # Discovery works for both the directory name and the qualified path.
+    assert _find_node(G, "process-order")
+    assert _find_node(G, "process-order/index.ts")
+    po = _find_node(G, "process-order/index.ts")[0]
+    assert G.nodes[po]["label"] == "process-order/index.ts"