Fisheries in Puerto Rico and the United States (US) Virgin Islands are predominately dependent on nearshore coral reef ecosystems and have suffered from historical overfishing. The unique characteristics of reef fisheries, including strong habitat dependence, susceptibility to coastal impacts, diffuse landing sites and strong multispecies and multigear interactions suggest that standard approaches to fisheries management, especially those typically considered by the US Regional Fishery Management Councils, would not be applicable. Current management authority is split between local and federal agencies; however, there exists no uniform context and direction to current management initiatives, which results in lost efficiencies and opportunities. Proposed here is a new vision for fisheries management that takes into consideration the local ecological and socioeconomic characteristics of fishing, is compatible with regional resources and capacity, is ecosystem based and targets full stakeholder participation. Only an ecosystem-based approach can lead fisheries management out of the trap of unrealistic data collection and analysis demands, while at the same time refocusing emphasis away from attitudes and practices that promote overfishing. Management must be based on first principles regarding the desired state of the ecosystem and initiate strategies based on these principles. The key management goal is not to maximize fisheries catch, but to maintain the ecosystem in a state that will lead to sustained production. First principles would include maintaining ecosystem integrity and function, protecting all habitats and water quality, applying the precautionary approach, monitoring reference points and recognizing that production has limits. Resulting management tactics include marine reserves (to meet multiple goals), closed spawning aggregations, gear restrictions to maintain trophic balance and habitats, targeted data collection and assessments, adopting co-management practices and using ecosystem or community-based metrics. Fisheries management must fully incorporate the tools, resources and methods available within coastal zone management and other environmental agencies, while standards within those programmes must protect ecosystem health. Implementation will require attending to structural barriers inherent within existing fisheries legislation and regulations, multiple jurisdictions and the current cultures of scientists, managers and fisherfolk. Initial efforts should focus on developing a common language and frame of reference for all stakeholders.