Medicinal plants are the source of biologically active compounds that are in constant demand for the pharmacological industry. Active production of plant secondary metabolites is possible only under optimal conditions of plant growth and development. The state of medicinal plants is controlled not only by genotype and environmental conditions but by the qualitative and quantitative composition of their microbiota as well. The study of the structure and function of the rhizospheric communities of medicinal plants is important for obtaining of high quality medicinal raw materials. Microorganisms are the constant companions of higher plants, which can be used as a medicinal raw material. The rhizosphere microbiota is highly specific, even between different varieties of the same plant species. Each plant species has a specific microbiome of the rhizosphere, depending on the existing soil community. The rhizosphere of medicinal plants is marked by a special highly specific microbiome due to the specificity of root exudates. Active cell secretion of the roots provides nutrient substrates with microorganisms that form strong associations both inside the root tissues and on the root surface as well as in the soil around the roots. The purpose of the research was to study the effect of medicinal plants of different systematic groups on the composition of the microbial communities of the rhizosphere. The experiments were conducted in 2018–2019 at the nursery medicinal plant plot of the Department of ecology and botany of Sumy National Agrarian University.