There has been no prior report on allelic variations of SLA class II loci in Korean native pigs. Here, we analyzed two important SLA class II genes, DQB1 and DRB1, in Korean native pigs (n = 65). DQB1 and DRB1 were PCR amplified from genomic DNA by using locus-specific oligonucleotides, and six alleles were identified for each locus. In DQB1, all six alleles were identical to those previously reported. However, we identified three new alleles in DRB1. The level of heterozygosity for DQB1 and DRB1 was 49 and 34%, respectively. Phylogenetic analyses showed that alleles from Korean native pigs were clustered in five distinct groups for DQB1 and four for DRB1. Finally, we defined 13 DQB1-DRB1 haplotypes by combining genotyping results and pedigree information. These results provide information on the genetic diversity of Korean native pigs and SLA systems.