This is the first study on coral diseases in the Wakatobi Marine National Park (WMNP), south-east Sulawesi. It aimed to provide baseline knowledge of coral disease prevalence and coral health in this remote region. Results indicate a low disease prevalence of 0.57% with only two known diseases occurring within the sampling unit, white syndrome (0.42%) and tumours (0.15%). They affected 15 taxonomic groups from a total of 32 taxonomic groups. The presence of black-band disease (BBD), skeletal eroding band (SEB) disease and Porites ulcerative white spot disease (PUWSD) was identified outside the study area. A large number of corals were affected by previously undescribed conditions (9.7% of colonies). The impact of lesions named as green spot, green band, pigmented spot, and flatworm infestation is not known and represents an important area for future studies.