Globally, maritime boundaries on oceans form the basis of governance and management of natural resources, yet the fish, and other marine resources neither conform nor confine to these artificial boundaries. As goods and services from marine life continue to retrogress under the intense human exploitation and changing global environment, resilience could be supported through establishment of a functionally connected network of marine reserves across maritime jurisdictions. While the establishment of protected areas within the exclusive economic zones (EEZ) is expanding, mechanisms that would allow governments to conserve marine areas beyond national jurisdictions are currently inadequate. Consequently, implementing marine reserves is largely confined within territorial waters, high connectivity among contiguous maritime zones notwithstanding. As the global focus shifts toward achieving sustainable development goals for the oceans, there is a need for region‐specific approaches to area‐based biodiversity conservation that extends the scope of protection to areas in the high seas beyond the EEZ. Using simulations of functional connectivity and seafloor geomorphology, we present and apply in the Western Indian Ocean (WIO) region a contextual approach to regional marine conservation planning to inform a more effective regional marine conservation across maritime zones.