The study was conducted to find out how the structure and diversity of microbiomes in buried soils differ from those in surface soils, and can analysis of microbial DNA from buried soils be used as a tool for paleoecological reconstructions. Samples were taken from buried soils under earthworks (burial mounds or earth fortifications) of different age, and from surface soils of the same area. Total DNA was extracted, and bacterial, archaeal and fungal abundance (by ribosomal genes qPCR) and prokaryotic biome structure (by 16S rRNA gene amplicon sequencing) were investigated. It has shown, that microorganisms abundance and species richness are decreasing in buried soils. Taxonomic structure of prokaryotes in buried soils differs significantly from that in surface soils. Very low relative abundance of Verrucomicrobia is the main difference of the buried soils microbiome structure. Obtained results show that microbiome structure is altered strongly by soil burial and hardly can be marker of ecological conditions in soil before earthworks. Nevertheless, some features of vertical distribution of microbiomes in soil profile (eg decrease of abundance from A to B horizon) remains unchanged in buried soils and can carry some information about native soil microbiome.