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By the example of studying the Early Holocene paleoalluvial soil (ancient man's site in Akhtsu Grotto, an overflow terrace of the middle reaches of the Mzymta River, Sochi Black Sea region), the efficiency of using a set of microbiological methods revealing the conditions of formation of the ancient paleoobject and the genesis of the geomorphology of the river valley was shown. The study of morphology and mesomorphology of the palaeo-soil allowed to assume its possible formation under the conditions significantly more hydromorphic in comparison with the modern ones. It is probable that earlier, at the beginning of the Holocene, this area was not a terrace, but a near-terrace, over-watered part of the river floodplain. Microbiological characteristics confirmed this assumption. The composition of the microbial community was identified from the isolated soil DNA of prokaryotic microorganisms (bacteria and archaea) by DNA metabarcoding. Groups and species of microorganisms-indicators reflecting the specificity of genesis of the studied soils were identified. Microbiological indicators of overwatered conditions were representatives of the phylum Planctomycetes of Phycisphaerae and Planctomycetia classes dominant in the microbiome (more than 1% of total DNA) and cyanobacteria of Chloroplast class of Streptophyta, Stramenopiles and Pseudanabaenale orders, as well as archaea (0.5% of total DNA) of Euryarchaeota phylum; Thermoplasmata class; Methanomassiliicoccaceae family, capable of methanogenesis. This species was not found in the microbial complex of the modern background soil. Indicator microorganisms identified as part of the prokaryotic community of palaeo-soils may potentially have useful applicable properties.