Background <p>Plant fitness and health owes to the complicated network of plant microbe interaction. These interactions confer the plants with systemic resistance. To evaluate the systemic resistance mechanism eight molecularly identified <i>Bacillus</i> strains were investigated in present study to mitigate the hazardous impacts of <i>Rhizoctonia solani</i> in tomato plant (<i>Lycopersicum esculentum</i>).</p> Methods and results <p>Experiment was designed with eight bacterial treatments along with fungal inoculation including positive healthy control and negative pathogenic control. Out of all selected bacterial strains <i>B. pumilus</i>, <i>B. subtilis</i> subsp. <i>spizizenii</i> and <i>B. sonorensis</i> displayed maximum improvement in tomato growth, reduction in disease severity instigated by <i>R. solani</i> infection by elevated levels of defense related antioxidant enzymes and induced systemic resistance. The induction of defense related response at transcriptomic level revealed a positive correlation in the activation of pathogenesis related protein <i>PR-1</i>, PR-2 (β1,3 glucanase), PR-3 (chitinase) and PR-6 (peroxidase). In addition to transcriptional changes, biochemical defense mechanisms at metabolic level were improved in the form of elevated level of PPO, POD, PAL activities, total phenolics and total soluble proteins in temporal manner. <i>B. pumilus</i>, <i>B. subtilis</i> subsp. <i>spizizenii</i> and <i>B. sonorensis</i> can be applied as potent biofertilizer as well as biocontrol agents to enhance plant growth and trigger systemic resistance against pathogen infection.</p> Conclusion <p>It can be possibly concluded from the data that these <i>bacillus</i> strains have great potential to be alternative biofungicide at commercial level.</p>