The draft genome sequence of strain Bacillus thuringiensis SS2 consists of 426 contigs assembled at the scaffold level, totaling 5,030,306 bp, and contains 5,288 putative PATRIC protein-coding genes, including genes responsible for total benzoate consumption, degradation of halogenated compounds, heavy metal tolerance/resistance, biosynthesis of secondary metabolites, and microcin C7 self-immunity protein.