Marine reserve design often involves a tradeoff between meeting conservation goals (persistence of fished populations) and minimizing economic costs (lost fishing grounds). Optimization tools such as Marxan navigate that tradeoff by finding reserve configurations that minimize economic costs while protecting some minimum fraction of fish habitat. However, typical Marxan implementations do not account for patterns of larval connectivity among reserves, a factor known to be the key to population dynamics. We show how connectivity information (self-recruitment and network centrality) can be incorporated into the optimization. We then used a spatially explicit population model to compare the performance of reserves designed using habitat information alone or including connectivity. Incorporating connectivity information improved reserve performance for some species but not others. We conclude that including connectivity information can improve reserve design algorithms, but it is essential to evaluate species’ population dynamics to determine which species will benefit from a given reserve network.