This research examines the function changes around the coral reef ecosystem caused by coral disease in Paraja Bay. The research aims to identify coral disease and the correlation between diseases and reef coral species. These identifications of coral diseases can be used to assess corals’ growth process, reproduction, and structural changes. The in-situ data was collected in February 2022 at 16 stations on each side of four small islands. The closeness relationship analysis was performed using PCA and XLstat. The results show that the disease prevalences in four small islands are varied, namely Badul Island (17.2%), Mangir Island (6.96%), Oar Island (2.66%), and Umang Island (4.86%) with an average of 7.91%. The coral diseases found in all stations were Trematodiasis and White Syndrome. Corals with Trematodiasis symptoms were Favia sp., Favites sp., and Platygyra sp., while ones with White Syndrome were Acropora sp., Favites sp., and Pavona sp. The existence of the diseases indicates the need for ecosystem restoration to include environmental aspects and community activities. This restoration action can accelerate the process of habitat and associated biota recovery.