Global trade of live shrimp for ornamental display has increased in popularity in recent years. International trade in live shrimp is subject to regulation of certain notifiable diseases listed by the World Organisation for Animal Health (WOAH), however there is also a risk of transboundary movement of new, previously unknown shrimp pathogens. Here we report the discovery of a new pathogen of wild jelly shrimp (Acetes sibogae australis) from northern Moreton Bay, Australia. Affected shrimp displayed grossly visible opacity of the hepatopancreas. Histology revealed infection by multinucleate plasmodia of a haplosporidian-like parasite in hypertrophied epithelial cells of all hepatopancreas cell types (R, B, F and E). In heavy infections, almost complete displacement of normal hepatopancreas tissue was observed. Although sporulation was not observed, infected jelly shrimp appeared terminally diseased, suggesting this parasite may influence shrimp population dynamics. A morphological and molecular phylogenetic investigation identified the parasite as a novel species of the order Haplosporida, and the parasite was described as Haplosporidium acetes n. sp. This was the first report of disease caused by a haplosporidian in wild Australian decapod crustaceans, and the first record globally of haplosporidiosis in sergestid shrimp. In addition, we found co-infection of a novel microsporidian parasite in the Enterocytozoon Group Microsporidia (EGM) infecting nuclei of hepatopancreatic epithelial cells in one shrimp. The microsporidian was phylogenetically distinct from Ecytonucleospora hepatopenaei (EHP) known to infect penaeid shrimp in Asia. Those importing shrimp for ornamental display purposes need to be aware of the potential risks from unknown pathogens.