Current ontologies’ upper-level taxonomic structure is often quite complicated and hard to understand. In this paper I show how the theoretical tools of so-called Formal Ontology, and especially the theory of identity, can help to formulate cleaner, more general, more rigorous, and more understandable upper-level ontologies. I focus in particular on some examples of multiple generalization, proposing a way of simplifying the domain structure by splitting some concepts according to different identity conditions, or by excluding them because of their limited organizational role.