The change in the composition of soil microbiota as a result of the cultivation of various crops in agrocenoses is currently of great interest. The authors studied the effect of the root system of transgenic tomato plants (Solanum lycopersicum L.) grown in soil culture on the microbial community in the rhizosphere. The results showed that as a result of the cultivation of transgenic plants with the choline oxidase gene, the microbial community composition in the rhizosphere has changed significantly. A significant increase in the proportion (73%) and species diversity (Shannon index 2.25) of actinobacteria in the soil root zone of tomato transgenic codA plants as compared with control plants (10% and 0.95, respectively) has been revealed. The content of pseudomonads and micromycetes is significantly reduced (25 and 12% in transgenic plants; 70 and 81% in control plants, respectively). Thus, genetically modified plants are able to influence the microbial community structure in the rhizosphere.