Marine biodiversity is increasingly threatened by habitat destruction, environmental changes, and overexploitation. Preventing reductions in biodiversity and promoting sustainable resource use requires new management strategies, more effective education, and strong research. There is a need to switch to less destructive and wasteful fishing methods to protect critical and sensitive habitats from development and overexploitation. Marine reserves, areas permanently protected from all extractive uses, are gaining widespread attention as an innovative tool for conserving biodiversity while maintaining healthy sustainable fisheries. Effective use of marine reserves requires the integration of scientific disciplines in fisheries, oceanography, computer science, system analysis, ecology, genetics, social science, and conservation. Marine reserves are an essential element of the draft management plan for the Florida Keys National Marine Sanctuary. The Sanctuary presents a unique opportunity to elucidate the relative impacts of fisheries exploitation and oceanographic processes in determining the biodiversity and abundance of reef organisms. Cooperative academic and governmental research will test critical scientific hypotheses in order to improve the state-of-the-art in marine resource management.