ABSTRACT: Coral diseases have contributed significantly to the decline of coral populations at both local and global scales. The island of Karimunjawa, 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 lesions assemblages on six sites within three designated zones, namely Tourism, Aquaculture, and Core zones. Our investigation aimed to determine a) the types, abundance, and patterns of coral lesions, b) the correlation between coral cover and lesion abundance, and c) 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 lesions were identified where the non-disease lesions from sediment damage (SED) was present, and also is the most prevalent (9.95%), followed by white syndrome (WS; 3.7%). A correlation was found between the cover of dominant coral taxa and the abundance of lesions (disease and non-disease) at all sites. Nevertheless, the mean lesion abundance from all zones falls from moderate to high categories. These findings present current data on the distribution of coral lesions and their patterns across the zones in 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.