Aotus nancymaae represents an animal model for the pre-clinical evaluation of blood-stage vaccine candidates against Plasmodium falciparum and Plasmodium vivax. We present here the nucleotide sequences of exon 2 and 3 of MHC-DPB1 genes. In a group of seven unrelated animals captured in the wild, three alleles of MHC-DPB1 exon 2 could be identified. Phylogenetic analysis shows that in contrast to Aona- DRB and - DQB, the Aona-DPB1exon 2 amino acid sequences cluster in a species-specific manner. No evidence could be found for the conservation of allelic lineages pre-dating the divergence of Old and New World monkeys. Additionally, two nucleotide sequences of MHC-DPB1 exon 3 could be identified differing in one synonymous base exchange. Phylogenetic analysis of Aona-DPB1exon 3 amino acid sequence shows that it clusters together with human sequences separately from the New World monkey Saguinus oedipus. Aona-DP heterodimers are expressed on the surface of Aotus cells, as detected by staining with a cross-reactive monoclonal antibody, and can therefore present antigenic peptides to the cellular immune system.