The article presents the results of analysis of biodiversity and spatial-functional structure of the microbial complex in the soil rhizosphere, and development of ways to regulate the number of phytopathogenic micromycetes in the rhizosphere of soybean plants in organic production. Varieties of plants of soy were grown using the biopreparation "Philazonit", which was developed in the company "Philazonit of Ukraine". The study determined the effect of phylazonite biopreparation on the mycobiome of the rhizosphere of soybean plants. The interaction of plants of soy varieties Kent and Suzir’ja with phytopathogenic micromycetes in conditions of the organic production in the Central Forest-Steppe of Ukraine (Research farm “Skvyrske” of Institute of Agroecology and Nature Management of the National Academy of Agrarian Sciences of Ukraine (IANM of the NAAS) was investigated. The number of phytopathogenic micromycetes in the rhizosphere of plants of different varieties of soy is determined depending on the variety and technology of its cultivation. It was established that the biopreparation Philazonit inhibits the formation of the number of phytopathogenic micromycetes in the rhizosphere of plants of the soy variety Suzir’ja and Kent during the growing season. It is proved that the representatives of genera: Alternaria, Fusarium, Penicillium, Aspergillus are dominated in the rhizosphere of plants of soy of both varieties. In the rhizospheres of plants of the soy Suzir’ja variety the representatives of genus Penicillium (32.8%) most often occurred. The smallest number of micromycetes were members of the genus Aspergillus (9.5%). In the rhizosphere of plants of the Kent variety dominated by representatives of the genera Alternaria and Fusarium (35.6% and 34.1% respectively). Representatives of the genus Penicillium were 15% and Aspergillus – 15.3% It is proved noted that during the studies there was a correlation between the development of micromycetes and the hydrothermal coefficient – in the flowering phase (r=0.8) and in the ripening phase (r =0.9) except for the germination phase