Actinobacteria are well known as a rich source of diversity of bioactive secondary metabolites.Kutzneria, a rare actinobacteria belonging to the familyPseudonocardiaceaehas abundance of secondary metabolite biosynthetic gene clusters (BGCs) and is one of important source of natural products and worthy of priority investigation. Currently,Kutzneria chonburiensisSMC256Thas been the latest type-strain of the genus and its genome sequence has not been reported yet. Therefore, we present the first report of new complete genome sequence of SMC256T(genome size of 10.4 Mbp) with genome annotation and feature comparison between SMC256Tand other publicly availableKutzneriaspecies. The results from comparative and functional genomic analyses regarding the phylogenomic and the clusters of orthologous groups of proteins (COGs) analyses indicated that SMC256Tis most closely related toKutzneriasp. 744,Kutzneria kofuensis, Kutzneriasp. CA-103260 andKutzneria buriramensis. Furthermore, a total of 322 BGCs were also detected and showed diversity among theKutzneriagenomes. Out of which, 38 clusters showing the best hit to the most known BGCs were predicted in the SMC256Tgenome. We observed that six clusters responsible for biosynthesis of antimicrobials/antitumor metabolites were strain-specific inKutzneria chonburiensis. These putative metabolites include virginiamycin S1, lysolipin I, esmeraldin, rakicidin, aclacinomycin and streptoseomycin. Based on these findings, the genome ofKutzneria chonburiensiscontains distinct and unidentified BGCs different from other members of the genus, and the use of integrative genomic-based approach would be a useful alternative effort to target, isolate and identify putative and undiscovered secondary metabolites suspected to have new and/or specific bioactivity in theKutzneria.