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Parasporal crystalline inclusion proteins of some Bacillus spp. are of paramount importance due to their insecticidal, nematocidal, and cancer cell killing capabilities. Here, we present a brief report of the complete genome sequence of Bacillus sp. BD59S, a bacterium that produced HeLa cell-killing parasporal crystalline inclusion proteins. From genome sequencing and assembly, we found that the bacterium has one circular chromosome and two large plasmids, pBTBD59S1 and pBTBD59S2. The size of the chromosome is 5283,933 bp with a 35.4% GC content, consisting of 5938 genes and 5550 protein-coding sequences (CDSs), 25 complete rRNAs (5S, 16S, 23S), 98 tRNAs, 5 ncRNAs, 260 pseudo-genes, and 356 subsystems. Complete plasmid sequence of pBTBD59S1 comprises a total size of 162,149 bp with 33.4% GC content, 192 CDSs, and 13 subsystems. The other plasmid pBTBD59S2, is 199,209 bp long with 32.9% GC content, 179 CDSs, and 11 subsystems. Analyses by NCBI microbial genome BLAST, phylogenetic genome tree, and BLAST ring image generator (BRIG) revealed that BD59S belongs to Bacillus cereus group, and is more close to B. thuringiensis. Further, the strain possesses 57.04 kDa and 54.42 kDa Cry protein-coding genes, which show significant similarities with cancer cell-killing parasporin proteins of B. thuringiensis strains. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-019-1849-7) contains supplementary material, which is available to authorized users.