Technical Abstract: The complete genome of the biocontrol antagonist Bacillus amyloliquefaciens AS 43.3 is reported. The 3.9 Mbp genome was sequenced, assembled, and annotated. Genomic analysis of the strain identified ten biosynthetic gene clusters encoding secondary metabolites associated with biocontrol activity. The analysis identified five non-ribosomal peptide synthetase clusters encoding three lipopeptides (surfactin, iturin, and fengycin), a siderophore (bacillibactin), and the antibiotic dipeptide bacilysin. In addition, three polyketide synthetase clusters were identified which encoded for the antibacterials, bacillaene, difficidin, and macrolactin. In addition to the non-ribosomal mediated biosynthetic clusters discovered, we identified a ribosomally encoded biosynthetic cluster that produces the antibiotic plantazolicin. To confirm the gene clusters were functional, cell-free culture supernatant was analyzed using LC-MS/MS. The technique confirmed the presence of all ten metabolites or their derivatives. The study suggests the strain is mostly likely a member of the B. amyloliquefaciens subsp plantarium clade. This study demonstrates the growing importance of applying genomic-based studies to biocontrol organisms of plant pathogens which can enable the rapid identification of bioactive metabolites produced by a prospective biological control organism.