diff --git a/bench/Makefile b/bench/Makefile
index 12b916fc..34280856 100644
--- a/bench/Makefile
+++ b/bench/Makefile
@@ -280,6 +280,7 @@ bench-string-exe:
 
 clean:
 	rm -f *.o bench-*.exe bench-*.s *~ massif.out.*
+	cd nucleotide && $(MAKE) clean
 
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