Dinoflagellates in the genus Hematodinium are important parasites of wild marine crustaceans, but are rarely reported in waters with salinities < 11 or from cultured crustaceans. Since 2005, the mud crab Scylla serrata, which is cultured along the coast of southeastern China, has suffered from an acute epizootic locally known as 'milky disease'. The disease mainly occurrs from September to November. The clinical signs are largely similar to those of crabs suffering from bitter crab disease (BCD) or pink crab disease (PCD), which are caused by parasites of the genus Hematodinium. To determine whether Hematodinium sp. is a pathogen of milky disease, histopathological examinations of mud crab haemolymph, hepatopancreas, heart and gill were conducted. In addition, previously reported Hematodinium molecular probes were applied to infected material. The results indicate that Hematodinium sp. is at least one of the main pathogens of milky disease. The salinity in S. serrata culture ponds was < 9. To our knowledge, this is the first report showing the Hematodinium infection in a cultured crustacean in low salinity water.