Strain Bacillus safensis DMB13 exhibiting protease and lipase activity was isolated from fermented kimchi in the previous study. Phenotypically, strain DMB13 showed no antibacterial activity. Thus, the complete genome sequence was analyzed to understand the phenotype of strain DMB13. The genome is 3,856,276-bp with a G+C content of 41.61 mol% and consists of a single circular 3,849,633-bp chromosome and one circular plasmids. Two genes related to bacteriocin production, skfF and skfG, were identified; however, six other genes in the skf operon were not detected. The genome includes 54 protease- and 5 lipase-encoding genes.