California has now largely completed a process for establishing marine protected areas (MPAs) that may be considered a model for other jurisdictions seeking to meet obligations under the Convention on Biological Diversity. In the Californian process, a team of scientists established guidelines on the size and spacing of MPAs, as well as requirements for habitat representation and replication. The final outcomes, in terms of proportion of the coast encompassed by MPAs and the distribution and sizes of MPAs, were largely a result of decisions taken by the advisory scientists, rather than by the designated decision makers. Future legislation must recognize the uncertainties associated with benefits of MPAs and specifically allow for adaptive management including explicit experimental tests of uncertainties. The science team should define at the outset the major uncertainties about impacts, and deliberate experimentation and adaptive management should be essential parts of each design. Future legislation should be much more specific about the objectives of the MPAs and specify the percentage of the area that should be set aside as MPAs. Finally, quantitative models rather than guidelines should be used to evaluate the consequences of alternative designs.