Abstract:CRISPR (Clustered regularly interspaced short palindromic repeats)/Cas (CRISPR associated proteins) is an acquired immune system found in bacteria and archaea that degrade target sequences of DNA from invading viruses or plasmids in a RNA-guided manner. CRISPR/Cas9 technology modified from type II CRISPR/Cas system has been developed as a strong genome editing and expression regulation tool, and widely used for studying gene function, metabolic engineering, synthetic biology, and other related fields. In this review, we summarize recent progress in development, classification, functional principle, applications and prospects of CRISPR/Cas9 technology in microbes.