Abstract: CRISPR (Clustered regularly interspaced short palindromic repeat sequences) is an adaptive immune system that confers resistance to bacteriophage or exogenous plasmid in bacteria. CRISPR/Cas9 technology developed from bacterial type Ⅱ CRISPR system has become a powerful genomic editing tool successfully used in most of existing creatures. Compared with Zinc-finger nucleases (ZFN) and Transcription activator like effector nucleases (TALEN) techniques, the advantages of CRISPR/Cas9 technical system are more simple, highly efficient, and cheaper. But for marine organisms, it is not widely used because of the difficulty of transferring exogenous DNA into most of marine animals. In this review, we introduced the developmental course, working mechanisms, prospects of CRISPR/Cas9 technology and the current status of its application in marine organisms. Moreover, we analyzed the potential application of dCas9 and the combination of Cas9 and optogenetic control method on studying gene regulatory mechanisms in marine animals, which might promote further application of CRISPR/Cas9 technology in more marine organisms in the near future.