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
@@ -124,6 +124,15 @@
         self._repo: Optional[hgutil.Repository] = None
         self._revision_nodeid_to_swhid: Dict[HgNodeId, Sha1Git] = {}
 
+        # keeps the last processed hg nodeid
+        # it is used for differential tree update by store_directories
+        # NULLID is the parent of the first revision
+        self._last_hg_nodeid = hgutil.NULLID
+
+        # keeps the last revision tree
+        # it is used for differential tree update by store_directories
+        self._last_root = HgDirectory()
+
         # Cache the content hash across revisions to avoid recalculation.
         self._content_hash_cache: hgutil.LRUCacheDict = hgutil.LRUCacheDict(
             self.config["content_cache_size"],
@@ -417,12 +426,25 @@
         Returns:
             the swhid of the top level directory.
         """
-        root = HgDirectory()
-        for file_path in rev_ctx.manifest():
+        prev_ctx = self.repo[self._last_hg_nodeid]
+
+        # TODO maybe do diff on parents
+        status = prev_ctx.status(rev_ctx)
+
+        for file_path in status.removed:
+            del self._last_root[file_path]
+
+        for file_path in status.added:
+            content = self.store_content(rev_ctx, file_path)
+            self._last_root[file_path] = content
+
+        for file_path in status.modified:
             content = self.store_content(rev_ctx, file_path)
-            root[file_path] = content
+            self._last_root[file_path] = content
+
+        self._last_hg_nodeid = rev_ctx.node()
 
-        directories: Deque[Directory] = deque([root])
+        directories: Deque[Directory] = deque([self._last_root])
         while directories:
             directory = directories.pop()
             self.storage.directory_add([directory.to_model()])
@@ -430,7 +452,7 @@
                 [item for item in directory.values() if isinstance(item, Directory)]
             )
 
-        return root.hash
+        return self._last_root.hash
 
 
 class HgArchiveLoaderFromDisk(HgLoaderFromDisk):