An automated method was developed for differentiating closely relatedB. cereus sensu lato(s.l.) species, especially biopesticideBacillus thuringiensis,from other human pathogens,B. anthracisandB. cereus sensu stricto(s.s.). In the current research, four typing methods were initially compared, including multi-locus sequence typing (MLST), single-copy core genes phylogenetic analysis (SCCGPA), dispensable genes content pattern analysis (DGCPA) and composition vector tree (CVTree), to analyze the genomic variability of 23B. thuringiensisstrains fromaizawai,kurstaki,israelensis,thuringiensisandmorrisoniserovars. The CVTree method was the best option to be used for typingB. thuringiensisstrains since it proved to be the fastest method, whilst giving high-resolution data about the strains. In addition, CVTree agrees well with ANI-based method, revealing the relationship betweenB. thuringiensisand otherB. cereus s.l.species. Based on these data, an online genome sequence comparison resource was built forBacillusstrains called theBacillusTyping Bioinformatics Database to facilitate strain identification and characterization.