The decline of many coral reef ecosystems in recent decades surprised experienced managers and researchers. It shattered old paradigms that these diverse ecosystems are spatially uniform and temporally stable on the scale of millennia. We now see reefs as heterogeneous, fragile, globally stressed ecosystems structured by strong positive or negative feedback processes. We review the causes and consequences of reef decline and ask whether management practices are addressing the problem at appropriate scales. We conclude that both science and management are currently failing to address the comanagement of extractive activities and ecological processes that drive ecosystems (e.g. productivity and herbivory). Most reef conservation efforts are directed toward reserve implementation, but new approaches are needed to sustain ecosystem function in exploited areas.