The evolutionary relationships among 10 taxa of deer from the four genera of the subfamily Cervinae (Cervus, Elaphurus, Axis, and Dama) were examined by a comparison of their electrophoretic types for 22 proteins. We analyzed the data using both phenetic and cladistic methods and found that the genera of the Cervinae were not monophyletic. The genus Cervus was split into two distinct groups with red deer, wapiti (C. elaphus ssp.), and sika (C. nippon) in one clade and sambar (C. unicolor) and rusa (C. timorensis) in another. There was a close genetic relationship between the genus Elaphurus and the red deer, wapiti, sika group, whereas sambar and rusa were more similar to members of the genera Dama and Axis than to the other members of their own genus. These findings contrast with the taxonomy of the species that is based largely on studies of comparative morphology. Our samples (n = 5) showed fixed allelic differences between wapiti and red, wapiti and sika, and red and sika samples at 3, 6, and 7 loci, respectively. Analysis of these protein loci in a wider range of C. elaphus and C. nippon subspecies could resolve debate over the evolutionary relationships of these taxa.