Predicted increases in disease with climate warming highlight the need for effective management strategies to mitigate disease effects in coral communities. We examined the role of marine protected areas (MPAs) in reducing disease in corals and the hypothesis that the composition of fish communities can influence coral health, by comparing disease prevalence between MPA and non-protected (control) reefs in Palau. Overall, the prevalence of diseases pooled, as well as the prevalence of skeletal eroding band (SEB), brown band disease (BrB) and growth anomalies (GAs) individually in major disease hosts (families Acroporidae and Poritidae), were not significantly reduced within MPAs. In fact, the prevalence of SEB was 2-fold higher within MPAs overall; however, the 4 studied MPAs were ineffective in enhancing coral assemblage or fish stock health. A negative association between the prevalence of SEB and richness of a fish species targeted by fishers in Palau highlights the potential role that well-managed MPAs could play in reducing SEB. The composition of coral communities and their susceptibility to bleaching also influenced the prevalence of disease on the studied reefs. The prevalence of diseases pooled and SEB were positively associated with the cover of major disease hosts (families Acroporidae and Poritidae), and the prevalence of BrB and bleaching were also positively associated. Although our study did not show positive effects of MPAs on coral heath, we did identify the potential for increased fish diversity within MPAs to reduce coral disease. Our study also highlights the complexity of relationships between fish assemblages, coral community composition and coral health on Indo-Pacific reefs.