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MHC genes are highly polymorphic as antigen presenting molecules for adaptive immune response in vertebrates. In this study, we evaluated the diversity of dog leukocyte antigen (DLA) class II genes among two Korean breeds, the Sapsaree and the Jindo, and three Chinese native breeds, Tibetan Mastiff, Pug, and Pekingese, and determined their genetic relationships. Sequence-based typing of DLA-DRB1 and DLA-DQB1 was performed in 138 dogs. We identified 27 alleles for DRB1 and 24 for DQB1, including five new alleles. DRB1*015:01 was shared among all five breeds and was a major allele for the Pug, Tibetan Mastiff, and Sapsaree. The observed heterozygosity for the five breeds ranged from 0.67 to 1.00 for DRB1 and from 0.80 to 1.00 for DQB1. A total of 40 DRB1-DQB1 haplotypes, including nine new haplotypes, were identified. Interestingly, most haplotypes (33/40, 82%) were specific to a single breed, and only seven were present in multiple breeds. Haplotype sharing analysis together with previously available data from 109 breeds revealed that compared to within region distances, Asian breeds were more distant than breeds from other regions. As a first report on the analysis of DLA genes of dog breeds in Korean peninsula, our results show that these breeds carry unique DLA class II haplotype lineages. Our results indicate that the diversity and breed specificity of DLA class II genes are much higher among East Asian breeds than among breeds from other regions.