Specimens of western pygmy perch, Edelia vittata Castelnau 1873, were submitted for examination because of the presence of black masses in the body wall in the abdominal area. The owner reported that approximately 10% of mature fish in one dam were affected. The masses had no apparent effect on the health of affected fish, but they were unsuitable for sale for aesthetic reasons. After necropsy and histological examination, the masses were found to be microsporidial xenomas within the abdominal cavity. Transmission electron microscopy results suggest that this microsporidian is a previously unreported species, because the melanised xenoma wall and internal structure of the spores differ from previously described species. The epidemiology of the parasite remains largely unknown and highlights the need for further surveys of the disease status and parasites of Australian native fish, especially those of interest to aquaculturists.