ABSTRACT: Coral diseases have contributed significantly to the decline of coral populations at both local and global scales. The Karimunjawa Archipelago, located off the coast of Java in Indonesia, is a marine national park with a zonation-based approach, designated by the local government due to its rich coral reef biodiversity. Unfortunately, there is a limited amount of research regarding the prevalence of coral diseases in coral reefs located on the islands. We analyzed the coral reef lesion assemblages at 6 sites within 3 designated zones, namely Tourism, Aquaculture, and Core zones. Our investigation aimed to determine (1) the types, prevalence, and patterns of coral lesions, (2) the correlation between coral cover and lesion prevalence, and (3) the susceptibility of coral taxa to lesions. A significant difference of 80.54% in the total number of coral lesions was observed between the tourism zone (24.34%) and the core zone (10.36%). Fourteen different lesion types were identified; among the non-disease lesions, sediment damage was the most prevalent (9.95%), followed by disease lesions caused by white syndrome (3.7%). A correlation was found between the cover of dominant coral taxa and the prevalence of lesions (disease and non-disease) at all sites. Mean lesion prevalence across all zones ranged from moderate to high categories. These findings present current data on the distribution of coral lesions and their patterns across zones around Karimunjawa Island. Research on the etiology and epidemiology of coral lesions should be promoted to identify ways to prevent the spread of coral diseases in Karimunjawa.