Coral health is an imperative aspect of coral reef ecosystems. Coral provides shelter, habitat, and nutrients for many organisms. Anthropogenic pollution that enters the oceans through runoff has negative effects on coral health such as inhibiting photosynthesis, growth, and reproduction. This study focuses on Cook’s and ‘Opunohu Bays in Mo’orea, French Polynesia. Each of the bays were assessed for substrate, algae, and coral composition as well as for a specific coral disease called Porites Trematosiasis (por trem) which is found exclusively on Porites coral heads. A total of forty-eight 10x10m plots were used to gather this information. The data indicate that sites were significantly better indicators for coral health and substrate difference as well as por trem than the bays, a comparison to past studies was made about the coral health and its change in the last twenty years. The coral health in Mo’orea has deteriorated in the past twenty years from natural causes such as cyclones, bleaching events, and Acanthaster planci outbreaks, but anthropogenic causes seem to have made a negative difference as well.