The parasitic dinoflagellate Hematodinium spp. infects a broad range of marine crustaceans. Its epidemics have impacted wild populations of various commercial fishery species around the world and the sustainability of mariculture in China. To study the epidemiology of Hematodinium spp. in marine crustaceans along the coast of China, we conducted a broad survey of wild and cultured stocks of major crustacean species in 2013 to 2015. Hematodinium sp. infections were identified in wild stocks of Portunus trituberculatus from Huludao, Laizhou, Qingdao, Yangtze River Estuary and Zhoushan, and Scylla paramamosain from Shantou; and cultured stocks of Portunus trituberculatus and Penaeus monodon from a polyculture pond in Qingdao. In the polyculture pond, Hematodinium sp. infections were observed in Portunus trituberculatus from June until October, with peak prevalence (up to 90%) observed in late July to early August. Furthermore, Hematodinium sp. infection was identified for the first time in the giant tiger prawn Penaeus monodon in the polyculture system during the disease outbreak. Phylogenetic analysis indicated that the Hematodinium isolate infecting Penaeus monodon was identical to the isolate infecting the co-cultured Portunus trituberculatus, and it was grouped into H. perezi genotype II together with the other isolates reported in China. The Hematodinium sp. isolated from Portunus trituberculatus appeared to have similar life stages as the H. perezi genotype III isolated from the American blue crab Callinectes sapidus. Our study indicates that outbreaks of Hematodinium disease can be a significant threat to the widely used polyculture system for decapods in China that may be particularly vulnerable to such generalist pathogens.