The degree of genetic polymorphism at the DRB3 locus in the major histocompatibility complex (Mhc) of the North American bison was investigated by PCR and DNA sequence analysis. Nine different alleles were characterized in a selected sample of 20 animals. The genetic distances between alleles were as large as usually found at highly polymorphic Mhc loci in other species. A comparative analysis of the DRB3 polymorphism in bison and cattle revealed an extensive sharing of sequence motifs. The result clearly shows a transspecies persistence of DRB3 allelic lineages in the two species. Consequently a significant amount of Mhc polymorphism has been maintained through the population bottleneck that bison experienced in the late nineteenth century. An analysis of the pattern of sequence polymorphism among bison and cattle DRB3 alleles strongly suggested that interallelic recombination has contributed significantly to the generation of allelic diversity at this locus.