Aquatic germplasm resources refer to genetic materials of aquatic animals and plants that possess actual or potential value, including species, subspecies, varieties, strains, etc. These resources hold significant economic, ecological, and scientific importance in the fields of fisheries and agriculture, serving as the foundation for aquaculture, genetic improvement, and biodiversity conservation. Aquatic germplasm resources encompass aquatic organisms such as fish, shrimp, shellfish, algae, and echinoderms, along with their genetic material. They are not only a core element supporting the sustainable development and international competitiveness of the aquaculture industry but also a strategic resource for safeguarding national food security, ecological security, and biodiversity. Building strengthened protection of aquatic germplasm resources, how to enhance the scientific utilization and innovative development of superior aquatic germplasm is both an urgent national need for biological and genetic diversity security and a pressing demand for high-quality, healthy aquatic products driven by growing public expectations. This review conducts a safety assessment from three perspectives: fundamental research on the utilization of aquatic germplasm resources, relevant technologies and platforms, and artificially cultivated and genetically improved germplasm. Based on a review of research progress in these areas, it analyzes existing problems within these three aspects and proposes recommendations for improving the utilization of aquatic germplasm resources. Future recommendations for enhancing the safety of aquatic germplasm resource utilization in China mainly include: strengthening the construction of a shared genomic resource platform for aquatic species based on China's independent intellectual property; increasing efforts to decipher the genetic mechanisms underlying economically important traits; advancing the development of low-cost, high-throughput, and intelligent technologies for precise phenotyping and genotyping, along with platforms for precise functional gene manipulation; and enhancing science popularization regarding transgenic and gene editing technologies while strengthening the protection of intellectual property rights for new varieties.