Cultivation of transgenic plants poses a threat to soil microflora. Genetically modified tomato plants with the choline oxidase gene have been found to have a greater species diversity. Despite the similarity of the phylum structure, many genera disappear from the rhizosphere of transgenic plants and new ones, not detected in the control, appear. Significant changes were found in the phyla Actinobacteria and Proteobacteria. In the former, polysaccharide destructors Acidothermus (family Acidothermaceae), Sporichthya (Sporichthyaceae), Arthrobacter (Micrococcaceae), Conexibacter (Conexibacteraceae) were found, with the disappearance of Gaiella (family Gaiellaceae) and Mycobacterium (Mycobacteriaceae). In the phylum Proteobacteria, complex polymer destructors Acidocella (family Acetobacteraceae) and Inquilinus (Rhodospirillaceae) disappeared; However, xenobiotic utilizers Pandoraea have emerged. In the long term, these changes may affect the rate of decomposition of plant litter and the availability of nutrients to plants.