The swine leukocyte antigen (SLA) is one of the most polymorphic regions of the pig genome, and not only is the important determinant of immune responses but also affecting other phenotypic characteristics. Previously, we reported high resolution genotyping methods for SLA-DQB1 and DRB1 using genomic PCR and direct sequencing. Here, we applied the strategy for the nucleotide sequence-based genotyping of SLA-DQA using the same principle. We selected 12 animals with non-redundant SLA-DQB1 genotypes to develop a genotyping method for tightly linked SLA-DQA to maximize the allelic diversity. We analyzed the sequences corresponding to partial intron 1 to exon 3 of 10 SLA-DQA alleles from them. We further typed 76 animals with diverse DQB1 and DRB1 genotypes, and resulted in determination of 14 DQA alleles from 36 genotypes. The observed level of heterozygosity for SLA-DQA was 67.05%. We also analyzed breeds differences in allele distribution by typing 140 animals of 7 pig breeds. From the analysis of the SLA-DQB1, DRB1 and DQA haplotype, we identified 34 SLA class II haplotypes and 25 of which were previously unreported. We also found four new SLA-DQA alleles from applying the method on 3 wild pigs. We expect that our method can be useful for the high resolution characterization and new allele identification of the SLA-DQA gene using field samples and thus contribute to understanding the importance of MHC polymorphisms in pigs.