diff --git a/src/sourmash/minhash.py b/src/sourmash/minhash.py
index c036fa6c3..448f64c00 100644
--- a/src/sourmash/minhash.py
+++ b/src/sourmash/minhash.py
@@ -742,6 +742,8 @@ def downsample(self, *, num=None, scaled=None):
             is_protein=self.is_protein,
             dayhoff=self.dayhoff,
             hp=self.hp,
+            skipm1n3=self.skipm1n3,
+            skipm2n3=self.skipm2n3,
             track_abundance=self.track_abundance,
             seed=self.seed,
             max_hash=max_hash,
@@ -764,6 +766,8 @@ def flatten(self):
                 is_protein=self.is_protein,
                 dayhoff=self.dayhoff,
                 hp=self.hp,
+                skipm1n3=self.skipm1n3,
+                skipm2n3=self.skipm2n3,
                 track_abundance=False,
                 seed=self.seed,
                 max_hash=self._max_hash,