The CRISPR/Cas genome editing technology, with its advantages of simplicity, high efficiency, and cost‐effectiveness, has become a key tool for dissecting gene function, knocking out harmful/undesirable genes, and repairing defective genes. It has also shown great potential in the genome editing of aquatic animals such as tilapia, carp, salmon, and sea urchins. Disease prevention and control are core areas of aquatic animal research and the aquaculture industry. Novel technologies based on CRISPR/Cas, such as rapid diagnostic kits for aquatic diseases and species‐specific drugs against parasites, have been developed in the disease diagnosis, treatment, and prevention of aquatic animals. Based on our work in these fields, this review summarizes the relevant new technologies and latest progress, aiming to provide readers with a quick and comprehensive understanding of the application status and future trends of CRISPR/Cas technology in the prevention and control of aquatic diseases and to provide a reference for related fields.