Lysinibacillus sphaericus is a heterogeneous species that includes strains that produce mosquitocidal toxin proteins. Herein, we report the 4.56-Mb draft genome sequence of the nonpathogenic L. sphaericus strain KCTC 3346(T), which provides clues for the phylogenetic reassessment of L. sphaericus species and an understanding of its physiological properties.