The currently living population of European bison (Bison bonasus) is divided into two genetic lines: Lowland line (LB) and Lowland-Caucasian line (LC). In order to compare the genetic diversity in two above mentioned lines the polymorphism of the major histocompatibility complex (MHC) DQA1 and DQA2 genes was analyzed. MHC genes are highly polymorphic and can therefore be used to asses genetic diversity in different species including endangered ones. The genetic polymorphism of exon 2 DQA1 and DQA2 genes was examined in 200 individuals of Lowland line and 56 individuals of Lowland-Caucasian line. The SSCP analysis revealed two alleles and two genotypes of exon 2 DQA1 gene and three alleles and four genotypes of exon 2 DQA2 gene. Frequency of genotypes of exon 2 DQA2 gene was significantly different (chi-square test p ≤ 0.05) between two genetic lines of European bison. Four haplotype configurations of DQA genes – DQA1, DQA2, DQA1/DQA2 and DQA1/DQA2_2 were observed. DQA1 haplotype confi guration was observed only in individuals belonging to LC and DQA1/DQA2_2 only in European bison from LB. Differences of frequency of haplotypes in two genetic lines were highly signifi cant (chi-square test p ≤ 0.01).