Effective genetic management of the ~700 aquatic species cultured globally should be addressed for aquaculture to make a significant contribution towards meeting the UN's Sustainable Development Goals. This article aims to identify the current status and challenges relating to the management of farmed aquatic genetic resources (AqGR) and to make recommendations for its improvement. The lack of information on the genetic status of many farmed species is a critical constraint and there is a need to characterize these resources and develop information systems and tools to monitor farmed types used for aquaculture and their wild counterparts. Risk assessment is needed when introducing non-native species and when managing native species including developed farmed types; policies need to be improved and increased awareness and training in risk assessment are required. To increase the uptake of selective breeding in aquaculture, there is a need for the development and adoption of better and more sustainable business models, including long-term financial instruments such as public–private partnerships. Training and technology transfer between aquaculture sectors can have significant impact, especially for lower-value species. Nationally and globally applicable instruments and regulations need to be adapted to AqGR and become operational and be effectively implemented by countries.