Tropical seagrass beds and coral reefs are among the most productive and diverse ecosystems on Earth and provide ecosystem services, such as fish production and coastal protection, and support livelihoods of millions of people. At the same time, these ecosystems are threatened globally by anthropogenic disturbances, such as overfishing, pollution and global warming. Implementation of marine protected areas (MPAs) is one of the main strategy to achieve conservation goals and has proven to restore biodiversity and fish stocks, at least on coral reefs. However, studies assessing protection effects on seagrass communities are scarce. Moreover, many MPAs are government-managed and increasingly criticized for excluding and marginalizing local communities. Therefore, MPAs that are managed by the communities themselves, i.e. community-managed MPAs, constitute a promising yet poorly studied alternative.

The aim of this thesis was to investigate ecological effects of government- and community-managed MPAs on seagrasses, corals, and their associated benthic and fish communities in the tropical seascape. We used a space-for-time replacement approach and surveyed coral and seagrass communities in fished areas, recently established community MPAs (1-6 years of protection) and old government MPAs (20-44 years) in coastal Kenya, East Africa. Results suggest that only a few years of protection in community MPAs can increase diversity of benthic communities (Paper I), and also protect economically valuable fish stocks (Paper II). Protection also appeared to induce a community shift, from dominance of pioneering and stress-tolerant coral and seagrass species in fished areas, to structurally complex climax species in old government MPAs (Paper I). Additionally, effects of protection on seagrass communities seems to be most apparent in the mid-lagoon by favoring seagrass species with high shoot density; an effect that was mostly caused by species turnover but also phenotypic plasticity. Meanwhile, effects in the shallow intertidal and reef zones were weak or non-existing (Paper III). Finally, a two-year field experiment suggests that a community MPA speeds up seagrass recovery and decrease sediment erosion following experimental disturbance, most likely by reducing additional disturbances (e.g. fishing practices) on recovering plants and sediments (Paper IV).

Based on these results I make three conclusions. First, MPAs seem to protect seagrasses in a similar way as they protect corals, suggesting that MPAs can aid local seagrass conservation. Seagrass beds should therefore be actively incorporated in marine spatial planning. Second, even though recently established community MPAs were not as effective as the old government MPAs, they appear to benefit both seagrass and coral communities (Paper I, II, IV). Given that previous studies show that they can also fulfill socio-economic community level-values (e.g. involvement in MPA design and enforcement), our findings emphasize their potential as a complement to government MPAs. Third, MPAs are an effective tool to protect seagrass and coral communities from local disturbances, particularly in mid-lagoon and reef areas, but they do not appear to protect the shallow intertidal seagrass beds (Paper III), possibly because of MPA-related tourism activities. This highlights the need for more detailed MPA evaluations, but also the need for more holistic conservation approaches, like integrated coastal zone management.