Designation of marine protected areas (MPAs) is increasing as humans seek to combat overexploitation of marine resources and preserve the integrity of the ocean’s unique biodiversity. At present there are over 1300 MPAs. The primary legal responsibility for the designation of MPAs falls to individual countries, but protection of the marine environment at large scales is also critical because ocean circulation does not honor legal boundaries and often exceeds the influence of any one nation or group of nations. There are many reasons for establishing MPAs; the papers we surveyed principally referred to scientific, economic, cultural, and ethical factors. Two approaches predominated: fisheries management and habitat protection. Although the major threat to terrestrial systems is habitat loss, the major threats to the world’s oceans are fisheries overexploitation, coastal development, and chemical and biological pollution. MPAs may provide conservation of formerly exploited species as well as benefits to the fishery through leakage of ‘surplus’ adults (spillover) and larvae (larval replenishment) across reserve boundaries. Higher order effects, such as changes in species richness or changes in community structure and function, have only been superficially explored. Because many MPAs are along coastlines, within shipping lanes, and near human centers of activity, the chance of chemical and biological pollution is high. Use of MPAs to combat development and pollution is not appropriate, because MPAs do not have functional boundaries. The ocean is a living matrix carrying organisms as well as particles and therefore even relatively environmentally sensitive uses of coastal ecosystems can degrade ecosystem structure and function via increasing service demands (e.g. nutrient and toxics transformation) and visitation. Whether an MPA is effective is a function of the initial objectives, the level of enforcement, and its design. Single reserves need to be large and networked to accommodate bio-physical patterns of larval dispersal and recruitment. Some authors have suggested that reserve size needs to be extremely large — 50–90% of total habitat — to hedge against the uncertainties of overexploitation. On a local scale, marine protected areas can be effective conservation tools. On a global scale, MPAs can only be effective if they are substantively representative of all biogeographic zones, single reserves are networked within biogeographic zones, and the total amount of area reserved per zone is 20% or greater. The current size and placement of protected areas falls far short of comprehensive or even adequate conservation objectives.