The Chinese concave-eared torrent frog (Odorrana tormota) was the first non-mammalian vertebrate demonstrated to both produce and perceive ultrasonic frequencies. Due to habitat degradation caused by human activity, currently, the species is at the edge of extinction. In this study, we demonstrated that the species harbors at least four expressed major histocompatibility complex (MHC) class II B loci. Four distinct intron 2 sequences and three intron 1 sequences were isolated from genomic DNA. Additionally, eight alleles were recovered from three cDNA samples, of which five could be assigned to three individual loci while the locus identity of the remaining three alleles could not be determined. Based on the intron sequences, locus-specific primers were designed for Odto-A, Odto-B, and Odto-C. Of these loci, Odto-B was monomorphic in Huangshan population (n = 32), and Odto-C displayed low allelic polymorphism with only three similar sequences obtained from partial individuals. In contrast, Odto-A showed high allelic diversity with 20 unique alleles recovered from the population. No inter- or intra-allele recombination was detected. However, 10 positive selected amino acid residues and an excess of non-synonymous substitutions were detected in the putative antigen binding sites (ABS), these results combined with trans-species evolution suggested some form of balancing selection that maintained higher allelic polymorphism for the locus. Our findings demonstrate that despite the effects of a severely shrinking population, O. tormota exhibits high polymorphism compared to other amphibians, both in terms of the allele number and diversity across the MHC class II B loci. J. Exp. Zool. (Mol. Dev. Evol.) 320B: 501–510, 2013. © 2013 Wiley Periodicals, Inc.