In marine environments, charismatic or economically valued taxa have been used as flagships to garner local support or international funds for the establishment and management of marine protected areas (MPAs). Seahorses (Hippocampus spp.) are frequently used as flagship species to help engender support for the creation of small community-managed no-take MPAs in the central Philippines. It is thus vital to determine whether such MPAs actually have an effect on seahorse abundance, reproductive status and size. A survey of seahorses inside and immediately adjacent to eight MPAs, and in four distant unprotected fishing areas, showed these MPAs had no significant effect on seahorse densities; although densities in and near MPAs were higher than in the distant fished sites, seahorse densities did not change over time. Seahorse size did show a marginal reserve effect, with slightly larger seahorses being found inside MPAs as compared to the distant unprotected fishing areas, but, in general, MPAs had little impact on seahorse size. Although MPAs may eliminate local fishing pressure, they may not reduce other threats such as pollution or destructive fishing outside the reserves. Other recovery tools, such as ecosystem-based management, habitat restoration and limits on destructive fishing outside of MPAs, may be necessary to rebuild seahorse populations. The effects of MPAs depend on species, as well as conditions outside the reserve boundaries. MPA management objectives must thus be clearly and realistically articulated to the communities, especially if support for an MPA was derived at least partly to conserve a particular flagship species.