This article explores the intersection of, and relationship between, the Biodiversity Beyond National Jurisdiction (BBNJ) Agreement and the Antarctic Treaty System (ATS). It examines the status of the Southern Ocean as an ‘area beyond national jurisdiction’ before analysing the application of the ‘not undermine’ principle to the ATS as developed in Article 5 BBNJ Agreement. The article examines the implications of the BBNJ Agreement in relation to environmental impact assessments, area-based protection, marine genetic resources and dispute resolution within the ATS. It argues that the thus far defensive approach of the Antarctic Treaty parties to the BBNJ Agreement is neither sustainable nor in the long-term interests of either agreement. It argues for positive engagement between the two regimes for the ultimate benefit of Southern Ocean governance.