The specificity of phylogenetic structure of prokaryotic community at different taxonomic levels has been studied in (i) the forest soil profile classified as Umbric Albic Luvisol profile and (ii) the humus horizons from anthropogenic changed soils. Predominant phyla of bacteria constituting from the humus horizons of anthropogenic changed soils as well as from Umbric Albic Luvisol were represented by Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, Proteobacteria and Verrucomicrobia. The analysis of microbiomes’ structure of soils has revealed that the humus horizons were characterized by a strong difference due to both (i) composition of bacterial phyla and their relative content and (ii) in positions occupied by representatives of individual phyla in microbial community in soil. Summarizing data, the structure of the microbial community in humus horizons at the taxonomic levels (phyla, class, order, family, genus) can be the most informative about the microbiome of in the anthropogenic-changed soils. The structure of microbial communities of soils’ humus horizons at different taxonomic levels was affected by the genetic traits of soils as well as the influence of anthropogenic factor, especially by soils alkalization. A variety of metabolism products entering urban soils also plays an important role. The features of a microbiome of urban soils are meant to be a sensible all-purpose indicator of their state.