MBI600 ( MBI600) is a recently commercialized plant-growth-promoting rhizobacterium (PGPR). In this study, we investigated the effects of MBI600 on the growth of tomato and its biocontrol efficacy against three main soilborne tomato pathogens (, , and f.sp. ). Furthermore, the root colonization ability of the MBI600 strain on tomato roots was analyzed in vivo with a yellow fluorescence protein ()-labeled strain, revealing strong colonization ability, which was affected by the root growth substrate. The application of MBI600 on tomato plants resulted in significant increases in shoot and root lengths. Transcriptional activation of two auxin-related genes ( and ) was observed. Single applications of MBI600 on inoculated tomato plants with pathogens revealed satisfactory control efficacy compared to chemical treatment. Transcriptomic analysis of defense-related genes used as markers of the salicylic acid (SA) signaling pathway ( and ) or jasmonic acid/ethylene (JA/ET) signaling pathway (, , and ) showed increased transcription patterns in tomato plants treated with MBI600 or . These results indicate the biochemical and molecular mechanisms that are activated after the application of MBI600 on tomato plants and suggest that induction of systemic resistance (ISR) occurred.