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For the first time, the allelic diversity of exon 2 of the DRB1 gene (class II of the major histocompatibility complex, MHC) was determined by NGS sequencing in natural populations of two species of the genus Allocricetulus: Eversmann’s hamster (A. eversmanni) and the Mongolian hamster (A. curtatus). These species are genetically close, but allopatric and demonstrate different habitat preferences. Eversmann’s hamster inhabits the steppes and is often associated with agrocenosis, while the Mongolian hamster occures semi-deserts and deserts, where anthropogenic pressure is practically absent. Our analysis revealed a significant effect of positive selection on the diversity of alleles of the DRB1 gene in both study species. However, Eversmann's hamster is characterized by a large average distance between alleles, but a smaller proportion of heterozygous individuals, while the Mongolian hamster is characterized by a larger individual variety of alleles. Thus, despite the extensive range of Eversmann’s hamster, we noted significantly less functional diversity of adaptive genes, which may be due to an increased anthropogenic exposure.