The study of living organisms in the Antarctic soils is one of the most priority areas of polar research. The essential role of microorganisms in soil-formation and biospheric processes implies the relevance of the study of the microbiome adaptations and its ecological patterns in a variety of Antarctic soils. The use of Illumina sequencing technique was applied for investigation of prokaryotic communities in soils not covered and covered by moss-lichen cover, and in soils in conditions of different degree of ornitogenic impact. The results obtained showed that Actinobacteriota were generally dominated on the places without moss-lichen cover, Bacteroidota - in the soils with well-developed organogenic horizon, including the group of ornithogenic soils. The studied microbiomes were also characterized by a significant proportion of Cyanobacteria - prokaryontic phylum, typical for the initial stages of soil formation. Biodiversity analysis showed that the main factor that formed the composition of prokaryotic community was the presence and amount of organic matter in the soil, while ornithogenic influence was of subordinate importance. The results obtained make a contribution to the study of the microbial ecology of the primary soils of Antarctica and the adaptive trends of the microbiome to the harsh conditions of ecosystems of polar regions.