Jiadong Township in Pingtung County is a high-density grouper raising area for growing out farmed grouper. In order to determine the disease-related problems that occur during the grow-out phase, we accepted cases for examination submitted by fish farmers from January to October of 2012. After finishing routing water quality measurements and clinical examinations, we also collected and sent samples to the laboratory and carried out subsequent pathological and molecular diagnosis. All the experimental data were analyzed in order to establish farmed grouper disease prevalence data. We collected 965 diseased grouper cases and categorized the data into types of poor water quality, parasitic disease, bacterial disease, viral disease and others. The disease prevalence rates ranging from highest to lowest were poor water quality (47.56%), parasitic disease (45.49%), bacterial disease (36.17%), others (12.75%) and viral (6.01%). The main reasons for the poor water quality were high nitrite concentrations, high ammonium concentrations, high organic matter concentrations and abnormal pH values. The prevalence rates of parasitic diseases from highest to lowest were Cryptocaryonosis, Datylogyriasis, Trichodinosis, sea lice infestation, leech infestation, Ambiphrya infestation, Amyloodiniosis, and Centrocestus infestation. Cryptocaryonosis was commonly found during the low-temperature season, and other kinds of parasitic diseases usually were associated with poor water quality. The bacterial diseases were divided into bacterial dermatitis (349 cases) and systemic infection/peritonitis (41 cases) based on external and internal infections, which were caused by Vibrio and Streptococcus, respectively. These two bacterial diseases were common during the high-temperature season. The total number of viral disease cases was 58, including cases caused by iridovirus and nervous necrosis virus. Among the cases, most were iridovirus. It also indicated the iridovirus infection commonly breaks out during the high-temperature season.