Background: Coral reefs are among the most diversified ecosystems in the world, but suffer from anthropogenic and natural disturbances, often causing a shift from coral to algal (or other benthic groups) dominated ecosystems. Linking benthic communities' information with water quality data is urgently needed to understand current and future changes in benthic dominance. This research examined possible environmental causes on the abundance of the zoanthid Palythoa tuberculosa on Okinawa Island in southern Japan. Various water parameters (temperature, dissolved oxygen, salinity, pH, particulate organic matter, chlorophyll a, NO 2 -N, NO 3 -N, PO 4 -P, NH 4 -N, and the distance to the river mouth) were recorded along with benthic community composition at eight locations. Results: Turf algae, coralline algae, or sand, rubble and rock dominated most locations in this survey. Coral coverage was moderate (10% to 40%). P. tuberculosa was generally low in abundance, but common at Mizugama (9% of the benthic community) and Oku (25%). Water parameters varied among sites. Salinity was the only parameter correlated with the abundance of Palythoa (R