North Atlantic right whales have one of the lowest levels of genetic variation at minisatellite loci, microsatellite loci, and mitochondrial control region haplotypes among mammals. Here, adaptive variation at the peptide binding region of class I and class II DRB-like genes of the major histocompatibility complex was assessed. Amplification of a duplicated region in 222 individuals revealed at least 11 class II alleles. Six alleles were assigned to the locus Eugl-DRB1 and 5 alleles were assigned to the locus Eugl-DRB2 by assessing segregation patterns of alleles from 81 parent/offspring pedigrees. Pedigree analysis indicated that these alleles segregated into 12 distinct haplotypes. Genotyping a smaller subset of unrelated individuals (n = 5 and 10, respectively) using different primer sets revealed at least 2 class II pseudogenes (with ≥ 4 alleles) and at least 3 class I loci (with ≥ 6 alleles). Class II sequences were significantly different from neutrality at peptide binding sites suggesting loci may be under the influence of balancing selection. Trans-species sharing of alleles was apparent for class I and class II sequences. Characterization of class II loci represents the first step in determining the relationship between major histocompatibility complex variability and factors affecting health and reproduction in this species.