diff --git a/preprocessing/nextclade/src/loculus_preprocessing/config.py b/preprocessing/nextclade/src/loculus_preprocessing/config.py
index d84d5403ca..62e358355b 100644
--- a/preprocessing/nextclade/src/loculus_preprocessing/config.py
+++ b/preprocessing/nextclade/src/loculus_preprocessing/config.py
@@ -60,6 +60,7 @@ class Config:
     nextclade_dataset_name: str | None = None
     nextclade_dataset_name_map: dict[str, str] | None = None
     nextclade_dataset_tag: str | None = None
+    nextclade_dataset_tag_map: dict[str, str] | None = None
     nextclade_dataset_server: str = "https://data.clades.nextstrain.org/v3"
     nextclade_dataset_server_map: dict[str, str] | None = None
 
diff --git a/preprocessing/nextclade/src/loculus_preprocessing/prepro.py b/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
index 13f9eef580..a850cd1fd4 100644
--- a/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
+++ b/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
@@ -838,10 +838,17 @@ def get_nextclade_dataset_server(config: Config, segment: SegmentName) -> str:
     return config.nextclade_dataset_server
 
 
+def get_nextclade_dataset_tag(config: Config, segment: SegmentName) -> str | None:
+    if config.nextclade_dataset_tag_map and segment in config.nextclade_dataset_tag_map:
+        return config.nextclade_dataset_tag_map[segment]
+    return config.nextclade_dataset_tag
+
+
 def download_nextclade_dataset(dataset_dir: str, config: Config) -> None:
     for segment in config.nucleotideSequences:
         nextclade_dataset_name = get_nextclade_dataset_name(config, segment)
         nextclade_dataset_server = get_nextclade_dataset_server(config, segment)
+        nextclade_dataset_tag = get_nextclade_dataset_tag(config, segment)
 
         dataset_dir_seg = dataset_dir if segment == "main" else dataset_dir + "/" + segment
         dataset_download_command = [
@@ -853,8 +860,8 @@ def download_nextclade_dataset(dataset_dir: str, config: Config) -> None:
             f"--output-dir={dataset_dir_seg}",
         ]
 
-        if config.nextclade_dataset_tag is not None:
-            dataset_download_command.append(f"--tag={config.nextclade_dataset_tag}")
+        if nextclade_dataset_tag is not None:
+            dataset_download_command.append(f"--tag={nextclade_dataset_tag}")
 
         logger.info("Downloading Nextclade dataset: %s", dataset_download_command)
         if subprocess.run(dataset_download_command, check=False).returncode != 0:  # noqa: S603