The aim of the work was to determine the quantitative, qualitative composition and taxonomic structure of the eubacterial complex in the rhizosphere of sugar beet under different fertilizer systems. Microbiological methods were used to determine the content of microorganisms in the rhizosphere of sugar beet. Molecular methods were used to determine taxonomic structure as well as metagenome of the eubacterial complex of microorganisms. In the agrocenosis of sugar beet under different fertilizer systems the representatives of such families were prevailed as Alcaligenaceae, Pseudomonadaceae, Nitrososphaeraceae, Gaiellaceae, Micrococcaceae, Solirubrobacteraceae, Streptomycetaceae, Intrasporangiaceae, Solimonadaceae, Syntrophobacteraceae, Xanthomonadaceae, Enterobacteriaceae, Nocardioidaceae, Hyphomicrobiaceae, Comamonadaceae. It was found that under the biological system of fertilizers the species diversity of soil microbiota increased due to phyla: Alcaligenaceae, Gaiellaceae, Solirubrobacteraceae, Streptomycetaceae, Solimonadaceae, Syntrophobacteraceae, Xanthomonadaceae, Enterobacteriaceae, Nocardioidaceae, Hyphomicrobiaceae, Hyphomicrobiaceae. It was detected that the basis of the eubacterial complex of sugar beet included representatives of phyla Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, Verrucomicrobia, Bacteroidetes, and the absolute dominants were Proteobacteria – 76.9%, Actinobacteria – 13,4 %.