Abstract Impacts from human-induced direct-use perturbations on coral colonies are on the rise. Despite significant incidences of coral disease on a global-wide basis, too few studies have verified the sources of diseases affecting coral colonies. To determine if branching coral communities are prone to infection with black band disease, brown band disease, and white syndrome, this study compared the prevalence of coral disease between Great Barrier Reef Marine Park Zones in the Great Barrier Reef Marine Park, Australia. We found evidence for coral disease on 9.06% of sites, with white syndrome being the most prevalent, found on 5.46% of sites, brown band found on 2.90% of sites, and black band found on 1.45% of sites. Coral disease of any kind, specifically black band and white syndrome, were significantly less abundant in areas where line fishing was permitted than where it was prohibited. Moreover, there was an interaction between fishing regulations and location, such that fishing regulations did not predict the presence of disease offshore, but inshore coral disease was significantly more prevalent where line fishing was prohibited than where line fishing was permitted. Coral disease was most frequently found in General Use, Scientific Research Open to the Public, and Marine National Park Zones; and reliably least commonly found in Habitat Protection, Conservation Park, and Preservation Zones. There were also differences among Marine Park Management Zones with coral disease most prevalent in the Cairns/Cooktown (Offshore) zone and least prevalent in the Mackay/Capricorn (Offshore) zone. Cairns/Cooktown (Offshore and Inshore) were the highest zones for black band and brown band, and Mackay/Capricorn (Inshore) was the highest management zone for white syndrome.