Systematic approaches to site selection for marine protected areas (MPAs) are often favored over opportunistic approaches as a means to meet conservation objectives efficiently. In this study, we compared analytically the conservation value of these two approaches. We locate this study in Danajon Bank, central Philippines, where many MPAs were established opportunistically based on community preference, with few if any contributions from biophysical data. We began by identifying the biophysical data that would have been available when the first MPA was created in Danajon Bank (1995). We next used these data with the reserve selection software Marxan to identify MPAs that covered the same area as is protected under the current set of MPAs (0.32% of the total study area) and that would protect the greatest number of conservation targets at the lowest cost. We finally compared the conservation value of the current MPAs to the value of those selected by Marxan. Because of the dearth of biophysical data available in 1995 and the small area currently under protection, Marxan identified multiple configurations of MPAs that would protect the same percentage of conservation targets, with little differentiation among sites. Further, we discovered that the costs of obtaining and analyzing these data to be used for conservation planning would have been large relative to resources typically available to conservation planners in developing countries. Finally, we found that the current set of MPAs protected more ecological features than would be expected by chance, although not as many as could be protected using a systematic approach. Our results suggest that an opportunistic approach can be a valuable component of conservation planning, especially when biophysical data are sparse and community acceptance is a critical factor affecting the success of an MPA.