To investigate genetic diversity of a major histocompatibility complex (MHC) gene in the brown bear (Ursus arctos) population on Hokkaido Island, northern Japan, we cloned and sequenced parts of exon 2 and intron 2 of the MHC class-II DQA gene from 32 brown bears. According to strict criteria for allele identification established by mammalian MHC nomenclature committees, four DQA types (Urar-DQA*01 to Urar-DQA*04) were identified. Of the four, however, Urar-DQA*04 had a 12-bp deletion not detected in a cDNA analysis, indicating that this is a pseudogene at a distinct locus generated by gene duplication. The nucleotide sequences of the other three DQA alleles, which were expressed (because detected from cDNA), were very similar, indicating lower DQA variation in the Hokkaido brown bear population than in other mammals. We attribute this low genetic diversity to (1) some limited effect of possible balancing selection; (2) bottlenecks and inbreeding after migration and isolation of the Hokkaido brown bear population from the Eurasian Continent; (3) a much slower evolutionary rate in DQA than in other MHC genes in the Hokkaido brown bear population.