During the winter of 2009, we observed an outbreak of severe respiratory disease in Symphysodon discus in a fish farm. The disease began with anorexia, respiratory distress and behavioral disorders and caused the death of all affected juveniles (80%) within a few days. Gill filaments were inflamed, hyperplastic and necrotic, and were infected with Sciadicleithrum variabilum. We amplified the cytochrome oxidase I (COI) gene of the monogenean using PCR and sequenced the gene as a molecular marker to rapidly identify the species. We demonstrated successful sequencing of the COI gene for S. variabilum identification, together with the need to monitor this pathogen in fish farms.