The genus Cimexomys ("bug mouse") was named by Sloan and Van Valen in 1965. Most remains are restricted to teeth. Synonyms include Eucosmodon sp., Stygimys sp. ("Styx mouse"), and possibly Mesodma. "Cimex" means "bug", with reference to the type locality of Cimexomys minor in the Bug Creek Anthills in Montana, USA.