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The coral reefs of the Coral Triangle provide sanctuary for the highest concentration of marine biodiversity in the world and support the livelihoods and protein needs of millions of people. The health and productivity of these reefs are in serious decline from numerous threats, ranging from local threats such as over fishing and pollution, to the global threat of climate change. Local threats reduce the resilience of coral reefs to withstand global impacts from climate change, resulting in deterioration of reef structure and the ability of these ecosystems to sustain their ecological interactions. We will assemble data from disparate sources to develop a framework for prioritizing between places and among specific conservation actions that cost-effectively mitigate proximate land- and sea-based threats to coral reefs and apply it to regions within the Coral Triangle. With the overall goal of supporting decision making, we will work in close collaboration with local managers and policy makers to synthesize this data and develop a framework that is capable of considering complex ecological, social, and economic dynamics relevant to the region. We will demonstrate its utility at local and regional scales and under different social and economic management constraints within the Coral Triangle. Typically, management decisions on the land and sea are made independently, without fully considering how terrestrial land-uses impact marine biodiversity. Our work is novel as it is the first example of using economic theory to balance decisions between land and sea-based management actions. This information will help guide decision makers in determining where, when, and how money would be spent efficiently to protect coral reefs, sustain protein needs, and foster livelihoods of millions, in the face of a changing climate.