Nucleotide sequence evolution of the mitochondrial cytochrome c oxidase subunit II (COII) gene was used to examine the molecular phylogenetics and evolution of the Bovinae, a subfamily within the mammalian order Artiodactyla. The COII gene was sequenced in representatives of three bovine tribes (Bovini, Boselaphini, and Tragelaphini) and the outgroup taxon Capra (subfamily Caprinae). Although the phylogenetic analyses grouped Bison as sister to Bos, the genus Bison was paraphyletic, with the American bison being most closely related to species of Bos rather than to the European bison. COII data also supported a close relationship between African (Syncerus) and Asian (bubalus) buffaloes, the monophyly of the tribe Bovini, and a sister-group relationship between the tribes Bovini and Boselaphini. Analysis of nucleotide substitutions in the COII gene prompted a system of differential weighting of nucleotide substitutions for inferring phylogenetic relationships across the range of divergence times examined here (2-20 million years). Rates of evolution in the COII gene are examined and compared to evolutionary rates in mtDNA tRNA/rRNA genes and the D-loop among other artiodactyl taxa.