Bacillus spp. have been shown to produce antimicrobial compounds called cyclic lipopeptides. Strains of Bacillus isolates from disease suppressive compost produce three families of lipopeptides, surfactins, fengycins and iturins, however not all the isolates produce all the lipopeptides. The genetics behind the production of these lipopeptides is not that well known. The objective of this study was to confirm the identity of the bacterial isolates using whole genome phylogeny and identify the Bacillus cyclic lipopeptide biosynthesis genes. Isolates of Bacillus subtilis, B. megaterium, B. badius and Brevibacillus borstelensis were used in this study. It was shown that the identity of the bacterial isolates resembled the identity assigned using 16S rRNA sequences, except for B. subtilis isolates CU12 and M9-3. It was determined that the B. subtilis isolates and the B. borstelensis isolate possessed the gene operons for the cyclic lipopeptides whereas B. megaterium and B. badius isolates did not.