The Bacillus sonorensis L12 draft genome sequence is approximately 4,647,754 bp in size with a G+C content of 45.2%. Over 86% of the genome contains protein-encoding genes, including several gene clusters for de novo biosynthesis of the nonribosomal lipopeptides iturin, bacitracin, and fengycin, which could mean that the strain exhibits antifungal effects.