Due to the development and increasing cultivation of genetically engineered plants as an integral part of modern agriculture, the biosafety of soil microorganisms, essential elements of soil fertility, quality, and stability, has been discussed. To reveal the effect of transgenic plants on soil bio-diversity, it is necessary to compare the microflora of transgenic and parental plants. In this study, second-generation GM sugar beet seeds rendered resistant to the propagation of Necrotic yellow vein virus of beets (BNYVV) via gene silencing in a field trial were compared to their parental plant by analyzing 16S rDNA metagenomes with the use of the Illumina MiSeq platform. Analysis of the alpha and beta diversity found some influence on bacterial communication of rhizosphere between non-transgenic and transgenic (including 211S3, 219S3, 228S3, and 231S6 cultivars) sugar beets. Based on the results of the research on alpha diversity, the transgenic 211S3 and 219 S3 cultivars showed a lower average than the control sample in the Cho, phylogenetic diversity, Cho1 bias correction, and the number of OTUs indexes; The transgenic 231S6 cultivar showed a significantly higher mean than the control sample in the Simpsons index. Also, in the study of beta diversity based on the Bray-Curtis distance algorithm, all 211S3, 219S3, 228S3, and 231S6 cultivars and control samples were positioned in one group. According to the Unweighted UniFrac distance algorithm, 219S3 and 231S6 cultivars were put together in one group, and 211S3 and 228S3 cultivars were classified into one group. A comparison of the bacterial genera showed a noteworthy reduction in relative abundance. While a few genera showed a significant decrease in terms of overall abundance, other genera that stabilize molecular nitrogen and motivate plant growth, such as Agrobacterium, Devosia, Mesorhizobium, Burkholderia, and Bradyrhizobium, showed a significant decrease compared to the control cultivar in all transgenic beets.