Hi,
You can use single feature class with subtypes, add subtype field say Species_1 and Species_2 are the subtypes and suppose you have added two codded value domains Habitat_1 (with possible values A, B, C) and Habitat_2 (with possible values A, D, E) in Geodatabase domain list.
Now apply domain "Habitat_1" to subtype "species_1" and domain "Habitat_2" to subtype "Species_2" in Subtype tab of your feature class properties dialog box.