Bacillus is a well-studied bacterial genus of Gram-positive and spore-forming bacteria, commonly soil-borne and plant-associated. Many Bacillus species produce a range of secondary metabolites and volatile organic compounds that are beneficial to plants through various mechanisms, such as pathogen suppression or plant growth promotion. Genome availability is the initial step in unlocking the beneficial metabolic potential of plant-associated Bacillus spp by enabling the identification of bioactive compound-producing gene clusters. Here we announce the draft genome assemblies of thirteen Bacillus spp isolated either from the root, leaf or stem tissue of citrus trees in areas of high (Florida) or low (California) Huanglongbing (HLB) disease pressure.