Quantitative accounting of microorganisms was carried out by seeding on nutrient media selected in accordance with their type. Thus, we have explored some features of development of pathogenic complex of microscopic fungi in soils of beet-growing farms in Almaty and Zhambyl regions. Soil microbial communities in two areas are represented by microorganisms such as bacteria genera: Pseudomonas, Bacillus, Mycobacterium, Mycococcus, Pseudobacterium, Lactobacterium. It is shown that Bacillus and Pseudomona prevail in soil samples. It is established that the dominant species of microorganisms are fungi genera: Fusarium, Alternaria, Penicillium which are a part of pathogenic complex that cause root decay. On the basis of the obtained data, a protective and stimulating composition for reducing the incidence of sugar beet seeds before sowing will be developed in soil samples No. 1-No. 4 of Almaty. The Fusarium genus prevailed in the Almaty Region, and Botrytis prevailed in the Zhambyl Region.