The study of the quantitative and qualitative composition of the soil microbiota, which adequately reflects the degree of anthropogenic load, can be applied as an indicator of assessment of the ecological status of the soil of anthropogenically transformed biogeocoenosis.The aim of the article is to analyze the species composition of micromycetes of drained soils of the Trubizh river Basin as an indicator of the ecological condition of the soil of different degrees of economic activity. For microbiological analysis samples of organogenic (lowland deep and medium peat soils) and mineral (meadow-chernozemic) soils were used. The samples selected from four experimental plots with different degrees of anthropogenic load. In particular, the first plot is a long-term use fallow (more than 15 years) on deep peatlands, the second one is a field with corn for grain on medium peatlands. The third plot is a field with post-harvest soybean residues on medium peatlands and fourth one is fallow with annual and perennial grasses on meadow-chernozemic soils. Soil samples were taken from the root layer at a depth of 0-5, 5-10 and 10-20 cm according to the current DSTU. Isolation of micromycetes was carried out by dilution method of soil with the object of estimation of the concentration (number of colonies, micromycetes). The count of micromycetes was estimated on surface of potato-glucose agar and Chapek's agar plates and was determined by the number of colony forming units (CFU). It was established that in the plot with increased anthropogenic impact (field with corn for grain on medium peatlands) the total number of isolated micromycetes was twice less than in plots of fallow lands and soybean. There was observed very poor species compositions (13 species). 2 species (15%) of Zygomycota, where predominant concentration was Mucor plumbeus in the soil layer 0-20 cm and 11 species (85%) of Ascomycota were found. In all plots, the basis of micromycete complexes was formed by fungi-destructors of plant remains and root secretions of the genus Penicillium. The micromycetes of drained soils of the Trubizh river Basin was presented the biggest phylum Ascomycota (83-95.5%) and the phylum Zygomycota (4.5-17%) also.