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Black scurf and stem canker caused by <i>Rhizoctonia solani</i> is a significant disease problem of potatoes. Currently, chemical methods are the primary means of controlling this pathogen. This study sought to explore an alternative approach by harnessing the biocontrol potential of a bacterial mix of <i>Bacillus subtilis</i> and <i>Bacillus amyloliquefaciens</i> against black scurf, and to determine their effect on rhizosphere microorganisms of soil microbiota. This study showed that these bacteria demonstrate antagonistic activity against <i>Rhizoctonia solani</i>. Reduced damage to potato plants during the growing season in Siberia was observed. The index of disease development decreased from 40.9% to 12.0%. The treatment of tubers with this mix of bacteria also led to a change in the composition of the rhizosphere microbiota (according to CFU, 16S and ITS sequencing). This effect was accompanied by a positive change in plant physiological parameters (spectrophotometric analysis). The concentration of chlorophyll in potatoes with the bacterial mix treatment increased by 1.3 fold (<i>p</i> ≤ 0.001), and of carotenoids by 1.2 fold (<i>p</i> ≤ 0.01) compared with the control. After bacterial mix treatment, the length of the aerial parts of plants was 1.3 fold higher (<i>p</i> ≤ 0.001), and the number of stems 1.4 fold higher (<i>p</i> ≤ 0.05). The yield of potatoes was increased by 8.2 t/ha, while the large tuber fraction was increased by 16% (<i>p</i> ≤ 0.05). The bacteria mix of <i>Bacillus subtilis</i> and <i>Bacillus amyloliquefaciens</i> suppressed the plant pathogenic fungus <i>Rhizoctonia solani</i>, and simultaneously enhanced the physiological parameters of potato plants. This treatment can be used to enhance the yield/quality of potato tubers under field conditions.