1. While conservationists, resource managers, scientists and coastal planners have recognized the broad applicability of marine protected areas (MPAs), they are often implemented without a firm understanding of the conservation science — both ecological and socio‐economic — underlying marine protection. The rush to implement MPAs has set the stage for paradoxical differences of opinions in the marine conservation community. 2. The enthusiastic prescription of simplistic solutions to marine conservation problems risks polarization of interests and ultimately threatens bona fide progress in marine conservation. The blanket assignment and advocacy of empirically unsubstantiated rules of thumb in marine protection creates potentially dangerous targets for conservation science. 3. Clarity of definition, systematic testing of assumptions, and adaptive application of diverse MPA management approaches are needed so that the appropriate mix of various management tools can be utilized, depending upon specific goals and conditions. Scientists have a professional and ethical duty to map out those paths that are most likely to lead to improved resource management and understanding of the natural world, including the human element, whether or not they are convenient, politically correct or publicly magnetic. 4. The use of MPAs as a vehicle for promoting long‐term conservation and sustainable use of marine biodiversity is in need of focus, and both philosophical and applied tune ups. A new paradigm arising out of integrated, multi‐disciplinary science, management and education/outreach efforts must be adopted to help promote flexible, diverse and effective MPA management strategies. Given scientific uncertainties, MPAs should be designed so one can learn from their application and adjust their management strategies as needed, in the true spirit of adaptive management. 5. It is critical for the conservation community to examine why honest differences of opinion regarding MPAs have emerged, and recognize that inflexible attitudes and positions are potentially dangerous. We therefore discuss several questions — heretofore taken as implicit assumptions: (a) what are MPAs, (b) what purpose do MPAs serve, (c) are no‐take MPAs the only legitimate MPAs, (d) should a single closed area target be set for all MPAs, and (e) how should policymakers and conservation communities deal with scientific uncertainty? Copyright © 2003 John Wiley & Sons, Ltd.

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