The MHC DQ region in nonhuman primates, as in humans, consists of α and β chains that are polymorphic with strong linkage disequilibrium between certain DQA-DQB alleles. Not only are contemporary HLA class II allelic variants present in evolutionarily distant species, but we demonstrate that linkages between loci also bear ancient roots. In unrelated baboons (Papio cynocephalus anubis) and family segregation analysis of pigtailed macaques (Macaca nemestrina) we found cis-linkages between DQA1*01 and DQB1*05 or *06, between DQA1*05 and DQB1*03, and between DQA1*03 and DQB1*03 alleles, all of which are also prominent in modern humans. In contrast, one linkage that has not been seen in humans, between DQA1*05 and DQB1*06 alleles, was also found. These patterns of selective linkage disequilibrium imply evolutionary mechanisms following the divergence of species that constrain the diversity of haplotypes which evolve.