An acute rise of unexplained mortalities (reaching 84,000 fish at one farm in 2002, 32%) was observed at a rainbow trout (Oncorhynchus mykiss) farm on the southeastern Black Sea coast from January to June for at least the last four years. Three rainbow trout farms on the same river system were surveyed for eight months to determine the occurrence and spread of the suspected causative agent, Hexamita salmonis. We found that this protozoan was endemic to the trout farms from December through late August. The main determinants of the incidence and intensity were water temperature (non-linear regression, r(2) = 0.77) and oxygen and nitrate levels (ANOVA, r(2) = 0.83). The mean intensity of the parasite gradually decreased while prevalence gradually increased from February to April at the farm with the highest values. There was no weight loss in infected fish compared to uninfected fish (p = 0.4). The downstream farm had a higher level of parasitic intensity than the upstream farm during the high risk season. Hexamitiasis was the main cause of the high mortality in May and June when water temperatures were around 6-13 degrees C. Prophylactic measures should be taken in systems where this parasite is endemic. This is the first report of hexamitiasis from Turkey.