Many countries are grappling with how to implement their obligations for regulating the access, use and transfer of aquatic genetic resources and technologies under both access and benefit sharing (‘ABS’) and intellectual property regimes. The urgency for regulation is clear because the aquatic environment is one of the last frontiers for bio-prospecting1 and the use of its genetic resources in aquaculture is hailed as a key to global food security.2 However, the details of regulation under the United Nations’ Convention on Biological Diversity (‘Convention’),3 the Nagoya Protocol (‘Protocol’)4 and the World Trade Organization’s (‘WTO’) Agreement on Trade-Related Aspects of Intellectual Property Rights (‘TRIPS’)5 are not clear. This article steps outside the recent calls for new mechanisms for ABS of aquatic genetic resources.6 Instead it provides insight into how uncertainties surrounding obligations for technology transfer and ABS of aquatic genetic resources under the Convention and Protocol may be influenced by the approach taken in national patent laws on such issues as research defences.7 This approach recognises the interdependence of TRIPS, the Convention and Protocol regimes which are regulating the same resources and which must necessarily evolve together to avoid legal uncertainty for the transfer of aquatic genetic resource technologies.