Abstract: Coral reef disease is one of the major causes of reef degradation and coral mortality in Panjang Island. The present study was carried out to assess inter-seasonal coral disease states present and the coral taxa affected on Panjang Island, Java Sea. Coral disease monitoring surveys were conducted in dry season (May) and rainy season (November) of 2013. The prevalence of coral disease on the reef building corals was calculated as the mean percentage of coral colonies affected by disease per 50 m2 transect quadrats. Results of the present study showed that mean prevalence for all diseases observed was 74.37±5.29% SE. Four disease states detected were Pigmentation Response (58.68±4.81% SE), White Plague (17.76±8.60% SE), Ulcerative White Spot (6.59±0.08% SE) and Yellow Band Disease (2.88±0.05% SE). A total of 386 coral colonies observed, 287 colonies were affected by diseases. The prevalences of disease in the coral genus were found to be 59.15±6.77% SE in Porites sp., 6.85±1.52% SE in Montipora sp., 6.83±1.01% SE in Favites sp., 4.81±0.20% SE in Acropora sp., 4.71±1.21% SE in Goniastrea sp. and 1.02±0.02% SE in Pocillopora sp. There were no significant seasonal variation (p>0.10) between prevalence in dry season (74,68±3.61% SE) and rainy season (74.07±8,39% SE). To our knowledge, this is the first study of quantitatively coral disease on Panjang Island, Java Sea, Indonesia. Since a large number of corals in Panjang Island were affected by diseases, it represents an important area for future studies.