Global overfishing indicates a need to define fisheries sustainability thresholds and identify social factors promoting successful management, but rates of fishing and factors mediating sustainability over long timescales are largely unknown. Here, we reconstruct fisheries yield for the entire period of human habitation (five to seven centuries) for two coral reef ecosystems with substantially different fisheries histories (Florida Keys and the Hawaiian Islands) and evaluate the management strategies associated with periods of sustainable fishing. This involved a mixed methods approach, in which we estimated yield by fishery sector (commercial, subsistence, recreational and aquaculture) and characterized management strategies associated with periods of sustained high yields. We found differences between the two locations, with Hawai‘i sustaining yields of more than 12 mt km−2 for four centuries prior to the arrival of Europeans. This period was characterized by adaptive management whose design and enforcement exhibited characteristics of common property resource governance systems, and which effectively protected reef habitat, vulnerable life-history stages for fish, and species with high susceptibilities to overfishing. Reefs in both Florida and Hawai‘i were exploited intensively after European contact, with sequential export-driven depletion evident in Florida over the past century. Today, both exhibit strikingly similar modern catch levels, with landings exceeding 10 mt km−2 and evidence of overfishing. Our results demonstrate that management strategies and social institutions that support strict enforcement by a local rule-making authority have had substantial impacts on fisheries yields in the past and suggest that long-term sustainability of fisheries is possible, although rare today.