At the UN Conference on Sustainable Development in Rio in June 2012, world leaders committed to the conservation and sustainable use of marine biological diversity in areas beyond national jurisdiction (the high seas). Our analysis of gaps in high seas management indicates that a paradigm shift to a more systematic approach will be needed to safeguard high seas biodiversity from mounting threats. Experience from terrestrial and coastal areas indicates that a systematic approach to conservation planning and management can help to maintain ecosystem health and productivity while enabling sustainable use. Our analysis further demonstrates that the current legal regime on the high seas is insufficient to realize these objectives: management institutions have neither an adequate mandate for integrated planning nor the ability to effectively coordinate across multiple management regimes. We identify key elements for future high seas management and posit that a two-pronged approach is most promising: the development of an improved global legal regime that incorporates systematic planning as well as the expansion of existing and new regional agreements and mandates. This combined approach is most likely to achieve the required ecosystem-based, integrated and science-based management that world leaders at Rio acknowledged should underpin ocean management.