The taxonomic position of Microbacterium chocolatum was evaluated through 16S rRNA gene sequence and genome-based analyses. The pairwise similarity of the 16S rRNA gene sequence retrieved from the genome data between Microbacterium aurantiacum KACC 20510T and Microbacterium chocolatum JCM 12412T was 99.3%, while between Microbacterium kitamiense JCM 10270T and M. chocolatum JCM 12412T was 99.4%. The similarity between M. aurantiacum KACC 20510T and M. kitamiense JCM 10270T was 100%. In the phylogenomic tree (based on 71 bacterial single-copy genes), M. aurantiacum KACC 20510T, M. kitamiense JCM 10270T and M. chocolatum JCM 12412T showed no genetic divergence. The average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) values among M. aurantiacum KACC 20510T, M. chocolatum JCM 12412T and M. kitamiense JCM 10270T were above the cut-off values (95-96% for ANI and 70% for dDDH) for species delineation. This study supports the previous reclassification of Microbacterium kitamiense Matsuyama et al. 1999 as a later heterotypic synonym of Microbacterium aurantiacum Takeuchi and Hatano 1998, and also proposes that Microbacterium chocolatum Takeuchi and Hatano 1998 is a later heterotypic synonym of Microbacterium aurantiacum Takeuchi and Hatano 1998.