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This study reports a disease outbreak among juvenile cobia (Rachycentron canadum) farmed in cages in the state of Rio de Janeiro, Brazil, caused by the dinoflagellate Amyloodinium ocellatum and the monogenean Neobenedenia melleni. Two thousand five hundred fish were stocked at 0.4 kg/m3 in a set of 12 m3 tanks, in autumn (mean weight 15.0 ± 7.3 g) and in winter (mean weight 43.0 ± 5.6 g). Freshwater baths were administered as a routine treatment, as the symptoms were detected followed by two collection samples. Firstly in May 2011 (n = 5) and secondly in September 2011 (n = 10). In the first sample, the prevalence of N. melleni on the body surface was 100% and the mean intensity was 42.0 ± 1.7, while in the second sample the prevalence was 60% with a mean intensity 3.0 ± 0.2 and mean abundance 1.8 ± 0.4. Amyloodinium ocellatum was only found in the second sample, at a prevalence 100% and mean intensity 46.8 ± 3.4. The cause of fish mortality was possibly associated with a decrease in fish resistance after the first contact with monogenean parasites, allied with respiratory difficulty caused by the presence of A. ocellatum in the gills.