Evolution and subsequent selection have had its effects on the MHC and KIR gene families in humans and non-human primate species. For instance, rhesus macaques, an animal species applied in preclinical research to model human diseases, have a diverse MHC and KIR repertoire. This diversity is reflected by extensive copy number variation, allelic polymorphism, high sequence homology, and expansion and contractions of haplotypes, which may complicate the genomic characterization. The PacBio sequencing platform allows us to efficiently characterize the MHC and KIR transcriptome in different primate species and identify novel genes and alleles. By using a family-based study design, we are able to define MHC and KIR haplotypes from segregation analysis.