Brevibacillus fortis LJQJ21 was isolated from the rhizosphere of pepper, which has a plant growth promoting effect and antagonistic activity against plant pathogens belonging to the fungi (Fusarium) and oomycetes (Phytophthora capsici). In order to characterise the molecular biocontrol mechanism, the genome of strain LJQJ21 was obtained. The analysis of the LJQJ21 genome indicates that the plant-associated B. fortis LJQJ21 is a rich source of antimicrobial compounds and could serve as a valuable starting point for the development of novel biocontrol agents.