Soil microbiome plays a significant role in the development of the soil profile and the implementation of key soil biochemical processes. Observed Arctic warming creates significant environmental risks, since permafrost soils contain a huge amount of organic matter, which is in potential risk to be released in the form of greenhouse gases. This work is aimed to investigate the microbiomes in soils of mature tundra and anthropogenically affected areas of the Yamal region using a high-throughput sequencing approach. The taxonomic analysis of the soil microbiomes revealed 33 bacterial and archaeal phyla, among which the dominant were Proteobacteria, Acidobacteria, Actinobacteria, Bacteroides, Chloroflexi, Cyanobacteria, Firmicutes, Gematimonadetes, Patescibacteria, Plantomycetes, Thaumarchaeota, Verrucomicrobia, and WPS-2. The analysis of alpha and beta diversities revealed that undisturbed soil is completely different from anthropogenically affected ones in terms of microorganism biodiversity. Soils of the urban zone of Salekhard were found to be different with regard to the number of operational taxonomic units and beta diversity. Herein the microbiome in the upper and lower layers of soil developed under strong technogenic influence (M19) was unequal both in quality and in quantity. At the same time, soils developed in the recreational zone of Salekhard showed less differentiation profile of microbiome (former crop field and former vegetable garden soils). Microbial communities in the mature tundra soil showed less differentiated microbiome composition.