The unprecedented global heatwave of 2014-2017 was a defining event for many ecosystems. Widespread degradation caused by coral bleaching, for example, highlighted the vulnerability of hundreds of millions of people dependent on reefs for their livelihoods, well-being, and food security. Scientists and policy makers are now reassessing long-held assumptions about coping with anthropogenic climate change, particularly the assumption that strong local institutions can maintain ecological and social resilience through ecosystem-based management, adaptation, and restoration. Governance is struggling to address the new normal as ecosystem assemblages transform to novel configurations. A central challenge for policy makers in the Anthropocene is navigating environmental crises and coping with societal insecurity and change. Ecosystem governance needs a new paradigm to embrace rapid change and shape future trajectories. In this Perspective, we focus on coral reefs as vanguards for governance transformation. We explain the spatial, temporal, and political dynamics of reefs as they respond to climate change and outline a new governance paradigm applicable to all ecosystems.