The great majority of marine protected areas (MPAs) fail to meet their management objectives. So MPAs can be effective conservation tools, we recommend two paradigm shifts, the first related to how they are located and the second related to how they are managed. MPAs are unlikely to be effective if they are located in areas that are subject to numerous, and often uncontrollable, external stressors from atmospheric, terrestrial, and oceanic sources, all of which can degrade the environment and compromise protection. MPA effectiveness is also limited by low institutional and community capacity for management and inappropriate size with respect to ecological needs. In particular, the check list approach to management does not ensure that key threats are dealt with, or that management expenditures provide a quantifiable return. We recommend a business planning approach to MPA management, in which managers focus on the viability of the management system, i.e. the ability of the MPA to provide ecological goods and services to its target users over the long term.