Global warming caused from the heavy consumption of fossil fuel is one of the biggest problems to be solved. Biofuel has been gained more attention as an alternative to reduce the consumption of fossil fuel. Recently, butanol produced from the genus Clostridium has been considered as one of the promising alternatives for gasoline, fossil based fuel. Nevertheless, the lack of the genome-engineering tools for the genus Clostridium is the major hurdle for the economic productionof butanol. More recently, genome engineering toolshave been developed for metabolic engineering of butanolproducingClostridium species, which includes genome scalenetwork model and genome editing tools on the basis of mobilegroup II introns and CRISPR/Cas system. In this study, thegenome engineering tools for butanol-producing Clostridiumspecies have been reviewed with a brief future perspective.