Bacillus subtilis, a gram-positive bacterium commonly found in soil, is an excellent organism for plant biocontrol. The B. subtilis KRS015, an endophyte isolated from the seed of Gossypium hirsutum "Zhongzhimian No. 2", has been proven as its antagonistic activity against diverse fungal pathogens of plants, including Verticillium dahliae, a fungal pathogen of Verticillium wilt in various plants such as cotton. Here, we report the complete genome sequence of B. subtilis KRS015. The size of the KRS015 genome is 4,331,506 bp. Fifteen gene clusters for antibiotics and secondary metabolites, and 412 genes involved in plant bacterial interactions were identified in this genome. These findings qualified the potential of B. subtilis KRS015 as a biocontrol agent and may help reveal the molecular basis of its antagonistic mechanisms.