The article presents the results of the analysis of biodiversity and spatial-functional structure of the microbial complex on the vegetative organs of soybean plants. Ways of regulation of the number of phytopathogenic micromycetes on vegetative organs of plants of different soybean varieties in the conditions of organic production have been developed. The interaction of Kent and Constellation soybean plants with phytopathogenic micromycetes in the conditions of organic production in the Central Forest-Steppe of Ukraine (Skvyra Research Station of Organic Production of IAP NAAS) was studied. The number of phytopathogenic micromycetes on vegetative organs of plants of different soybean varieties depending on the variety and technology of its cultivation was determined. It has been experimentally proven that the biological product Filazonit controls the formation of phytopathogenic micromycetes on the vegetative organs of Kent and Constellation soybean plants during ontogenesis compared to the control and ranges from 0.3 to 3.3 thousand CFU/g of green mass depending on the variety. It was found that the vegetative organs of soybean plants of both varieties are dominated by representatives of the genera Cladosporium (C. herbarum Lket Gray), Alternaria, (A. alternate (Fr.) Keissl.), Fusarium (F. grameniarum Schleht), Aspergillus (A. flavus) Link.), Sclerotinia (S. sclerotiorum (Lib.)). It is determined that the number of phytopathogenic micromycetes in the mycobioma of vegetative organs of soybean plants depends on the variety and technology of its cultivation. The relationship between the development of micromycetes and the use of biological product Filazonit, as in the seeds of soybean varieties Constellation (germination phase — H05=0.5 and H05=0.3; flowering phase — H05=0.4 and H05=0.3), and on the Kent variety (seedling phase — H05=0.9 and H05=0.7; flowering phase — H05=0.8 and H05=0.6). The relationship between the development of micromycetes and the hydrothermal coefficient — in the germination phase and in the flowering phase.