diff --git a/malariagen_data/anoph/genome_features.py b/malariagen_data/anoph/genome_features.py
index ed4cc4c39..2bf315e4f 100644
--- a/malariagen_data/anoph/genome_features.py
+++ b/malariagen_data/anoph/genome_features.py
@@ -68,6 +68,14 @@ def _geneset_gff3_path(self):
 
     def geneset(self, *args, **kwargs):  # pragma: no cover
         """Deprecated, this method has been renamed to genome_features()."""
+        import warnings
+
+        warnings.warn(
+            "geneset() is deprecated and will be removed in a future version. "
+            "Use genome_features() instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         return self.genome_features(*args, **kwargs)
 
     def _genome_features(self, *, attributes: Tuple[str, ...]):
diff --git a/malariagen_data/anoph/snp_data.py b/malariagen_data/anoph/snp_data.py
index 0c2549c41..a5fe91fec 100644
--- a/malariagen_data/anoph/snp_data.py
+++ b/malariagen_data/anoph/snp_data.py
@@ -1380,6 +1380,14 @@ def _snp_calls(
 
     def snp_dataset(self, *args, **kwargs):  # pragma: no cover
         """Deprecated, this method has been renamed to snp_calls()."""
+        import warnings
+
+        warnings.warn(
+            "snp_dataset() is deprecated and will be removed in a future version. "
+            "Use snp_calls() instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
         return self.snp_calls(*args, **kwargs)
 
     def _prep_region_cache_param(