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The mammalian major histocompatibility complex (MHC) plays important roles in pathogen recognition and disease resistance. In the present study, the coding sequence and the 5′- and 3′-untranslated regions of MHC class II DR alpha chain (the DRA gene) from rare gayal and gaytle were cloned and analyzed to dissect structural and functional variations. The nucleotide and amino acid sequences for the DRAgenes in gayal (Bofr-DRA) and gaytle (Bofr× BoLA-DRA) were almost identical to those for cattle and yak (99%). Compared to yak, two amino acids substitutions in the signal peptide (SP) domain for gayal were found within all Bosanimals. Except for only one replacement in the amino acid within the α2 domain of the DRA protein in gayal, the additional residues were highly conserved across the species investigated. The 20 peptide-binding sites (PBS) of Bofr-DRAand Bofr× BoLA-DRAwere essentially reserved in the α1 domain among all species investigated. The lesser degree of substitution in Bofr-DRAis concordant with the concept that the DRAgene is highly conserved among all mammals. The very high degree of conservativity of the DRAgene among ruminants, including gayal, suggests its recent evolutionary separation.