Marine diseases represent a significant threat to wild organisms and the ecosystem services they support, yet studies often consider only disease impacts to aquaculture. In eastern Australia, the Sydney rock oyster (Saccostrea glomerata) aquaculture industry is increasingly affected by outbreaks of QX disease caused by parasitic Marteilia sydneyi. The present study considered impacts of M. sydneyi infection on the structure of wild-oyster populations that are dominated by S. glomerata, but that may also include the non-native Pacific oyster, Crassostrea gigas. In the Hawkesbury River Estuary, where cultured S. glomerata has experienced up to 98% QX-induced mortality, we found that disease prevalence was comparatively low among wild S. glomerata, peaking at 14%, and annual infections did not cause seasonal patterns of mortality. Furthermore, C. gigas, a competitor of S. glomerata that is not susceptible to QX disease, was not consistently more abundant at sites with than without the parasite. Overall, our results indicated that relative to cultured counterparts, wild S. glomerata in the Hawkesbury River Estuary is minimally affected by QX disease. Nevertheless, our study showed that diseases of aquaculture stocks have the capacity to infect wild populations, and that longer-term assessment of wild populations at risk is essential.