The rhizosphere isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome of the Bacillus methylotrophicus KACC 13015 T (= CBMB205T) . Comparative genomic analysis showed only minor differences between this strain and the genome of the Bacillus amyloliquefaciens subsp plantarum type strain, with the genomes sharing approximately 95% of the same genes. The results of morphological, physiological, chemotaxonic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of Bacillus amyloliquefaciens subsp plantarum FZB42T (=DSM 23117T =BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to Bacillus methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies Bacillus amyloliquefaciens subsp plantarum should be reclassified as a later heterotypic synonym of Bacillus methylotrophicus.