diff --git a/swh/loader/mercurial/from_disk.py b/swh/loader/mercurial/from_disk.py
--- a/swh/loader/mercurial/from_disk.py
+++ b/swh/loader/mercurial/from_disk.py
@@ -47,7 +47,7 @@
 TEMPORARY_DIR_PREFIX_PATTERN = "swh.loader.mercurial.from_disk"
 
 EXTID_TYPE = "hg-nodeid"
-
+EXTID_VERSION: int = 1
 
 T = TypeVar("T")
 
@@ -268,13 +268,13 @@
         )
 
     def _get_extids_for_targets(self, targets: List[bytes]) -> List[ExtID]:
-        # Get all Mercurial ExtIDs for the targets in the latest snapshot
+        """Get all Mercurial ExtIDs for the targets in the latest snapshot"""
         extids = [
             extid
             for extid in self.storage.extid_get_from_target(
                 identifiers.ObjectType.REVISION, targets
             )
-            if extid.extid_type == EXTID_TYPE
+            if extid.extid_type == EXTID_TYPE and extid.extid_version == EXTID_VERSION
         ]
 
         if extids:
@@ -461,7 +461,11 @@
         if from_cache is not None:
             return from_cache
         # The parent was not loaded in this run, get it from storage
-        from_storage = self.storage.extid_get_from_extid(EXTID_TYPE, ids=[hg_nodeid])
+        from_storage = [
+            extid
+            for extid in self.storage.extid_get_from_extid(EXTID_TYPE, ids=[hg_nodeid])
+            if extid.extid_version == EXTID_VERSION
+        ]
 
         msg = "Expected 1 match from storage for hg node %r, got %d"
         assert len(from_storage) == 1, msg % (hg_nodeid.hex(), len(from_storage))
@@ -546,7 +550,14 @@
             object_type=identifiers.ObjectType.REVISION, object_id=revision.id,
         )
         self.storage.extid_add(
-            [ExtID(extid_type=EXTID_TYPE, extid=hg_nodeid, target=revision_swhid)]
+            [
+                ExtID(
+                    extid_type=EXTID_TYPE,
+                    extid_version=EXTID_VERSION,
+                    extid=hg_nodeid,
+                    target=revision_swhid,
+                )
+            ]
         )
 
     def store_release(self, name: bytes, target: Sha1Git) -> Sha1Git:
diff --git a/swh/loader/mercurial/tests/test_from_disk.py b/swh/loader/mercurial/tests/test_from_disk.py
--- a/swh/loader/mercurial/tests/test_from_disk.py
+++ b/swh/loader/mercurial/tests/test_from_disk.py
@@ -26,7 +26,7 @@
 from swh.storage import get_storage
 from swh.storage.algos.snapshot import snapshot_get_latest
 
-from ..from_disk import HgDirectory, HgLoaderFromDisk
+from ..from_disk import EXTID_VERSION, HgDirectory, HgLoaderFromDisk
 from .loader_checker import ExpectedSwhids, LoaderChecker
 
 VISIT_DATE = parse_visit_date("2016-05-03 15:16:32+00")
@@ -613,3 +613,19 @@
         "skipped_content": 0,
         "snapshot": 2,
     }
+
+    snapshot = snapshot_get_latest(swh_storage, repo_url)
+
+    # filter out revisions from that snapshot
+    revision_ids = [
+        branch.target
+        for branch in snapshot.branches.values()
+        if branch.target_type == TargetType.REVISION
+    ]
+
+    # Those revisions should have their associated ExtID version to EXTID_VERSION
+    extids = swh_storage.extid_get_from_target(ObjectType.REVISION, revision_ids)
+
+    assert len(extids) == len(revision_ids)
+    for extid in extids:
+        assert extid.extid_version == EXTID_VERSION