The dispersal of plant pathogens is a threat to the global economy and food industry which necessitates the need to discover efficient biocontrol agents such as bacteria, fungi, etc., inhibiting them. Here, we describe the strain b12.3 isolated from the soil of Olkhon Island in Lake Baikal, Russia. By applying the co-cultivation technique, we found that the strain inhibits the growth of plant pathogens, such as the bacteria , , and as well as the fungus . To elucidate the genomic fundament explaining these activities, we leveraged next-generation whole-genome sequencing and obtained a high-quality assembly based on short reads. The isolate bore seven known BGCs (biosynthetic gene clusters), including those responsible for producing bacillibactin, fengycin, and petrobactin. Moreover, the genome contained insecticidal genes encoding for App4Aa1, Tpp78Ba1, and Spp1Aa1 toxins, thus implicating possible pesticidal potential. We compared the genome with the 50 closest assemblies and found that b12.3 is enriched with BGCs. The genomic analysis also revealed that genomic architecture corresponds to the experimentally observed activity spectrum implying that the combination of produced secondary metabolites delineates the range of inhibited phytopathogens Therefore, this study deepens our knowledge of the biology and ecology of residing in the Lake Baikal region.