The Karimunjawa Marine National Park, situated in the Java Sea, Indonesia, is renowned for its rich biodiversity and lively coral reefs. However, amidst the backdrop of this natural beauty, concerns have been raised regarding the potential impacts of shipping activities on the health and diversity of these fragile ecosystems. The increase in maritime traffic, including commercial vessels, tourist boats, and fishing vessels, traversing through the Karimunjawa Marine National Park, raises significant environmental concerns. The movement of these vessels, especially along specific shipping routes, has the potential to disturb and damage coral reefs through various mechanisms. Hence, this study aimed to investigate the possible impacts of shipping routes on the coral abundance and diversity and the coral health in the Karimunjawa Islands, Java Sea, Indonesia. This study categorized ship routes into West Route, East Route, and Non-Route and assessed coral health and diversity across 15 islands. Key metrics analyzed included coral disease prevalence, coral cover, diversity index, species richness, relative abundance, and evenness, using 15 × 2 m belt transects at 3 and 8 m depths with three repetitions each. Statistical analysis revealed significant differences in coral abundance and species richness among ship-route groups, but no significant depth-related differences. These results suggest that while shipping routes affect certain aspects of coral health and diversity, other factors may be more influential in shaping coral disease prevalence and overall diversity in Karimunjawa reefs. [ABSTRACT FROM AUTHOR]