The taxonomy status of genus Amycolatopsis which produced many important antibiotics is controversial due to the diverse phylogeny and physiology of its member species.The complete genomes of the antibiotic producing bacteria Amycolatopsis mediterranei,Amycolatopsis orientalis and Amycolatopsis japonica as well as the methanol-utilizing bacterium Amycolatopsis methanolica 239T revealed their common circular chromosomes varying in sizes.They presented abroad specmum of core/quasi-core/non-core genome configurations accompanied with different kinds of episomes,which inferred extensive horizontal gene transfer along evolution with biased chromosomal localization.Phylogenetic analyses based on 16S rDNA and genus core genes re-classified the 59 species of Amycolatopsis into three major branches,the mesophilic and thermophilic A.Orientalis subclade(AOS),the mesophilic Amycolatopsis taiwanensis subclade(ATS)and the thermophilic A.methanolica subclade(AMS)with their distinct temperature tolerance features correlated well with corresponding genetic variations in encoding compatible solutes.Most of the chemotaxonomic properties of the genus are reconfirmed based on genotypic variations leading to enriched biological knowledge related to primary metabolismsand the chemical compositions of the bacteria.Among those,complete pathways attributable to the special facultative methylotrophic physiology of A.methanolica including both the mdo and mscR encoded methanol oxidation and the hps and hpi encoded ribulose monophosphate cycle for formaldehyde assimilation are comprehensively identified.The rich secondary metabolites resources of Amycolotopsis species,particularly those of AOS subclade,can now be readily studied at the genomics level,ease for novel functional characterizations and improvement of productivities via revealing corresponding regulatory mechanisms.The genome research of the Amycolotopsis genus has provided an example which indicates how bacterial taxonomy will no longer be seen as a laborious and lagging science but will become an exciting discipline based on ever increasing biological knowledge enriched by the genomics-based genetic studies.