Biotechnology is crucial for the sustainable development of the aquatic seed industry. Therefore, improving the innovation capability in aquatic breeding and making seed sources independent are significant for ensuring food security in China. This study summarizes the development status and problems of aquatic breeding in China and analyzes the status of research and application of seven types of biotechnology for aquatic breeding, namely, transgenic breeding, ploidy breeding, molecular-marker-assisted breeding, genomic selection breeding, genome editing breeding, molecular design breeding, and germline stem cell transplantation; future research and development demand for these technical fields in China is further analyzed. Moreover, future development goals and major tasks are suggested, including collecting, preserving, and accurately identifying excellent germplasm resources of aquatic organisms, profoundly analyzing the genetic basis and regulatory mechanism of critical traits, developing efficient and accurate breeding technologies, and achieving breakthroughs in the creation of new varieties. Furthermore, following suggestions are proposed: optimizing development policies of the aquatic seed industry, promoting technological innovation in aquatic breeding, establishing platforms for aquatic variety creation and transformation, and setting up special projects to accelerate technological innovation and development of the aquatic seed industry.