The phylum Perkinsozoa includes well-known parasites of commercially important species of molluscs in aquaculture, such as Perkinsus marinus, a virulent pathogen of the eastern oyster, Crassostrea virginica, and in wild populations in many marine ecosystems throughout the world. These parasites are responsible for significant losses in aquaculture production. For this reason, much research has already been conducted with these parasites. The zoospores of Perkinsus secrete several classes of proteases which facilitate the digestion of host tissues. The host can respond by producing protease inhibitors and by mounting cellular immune responses as defence strategies. The impacts of infectious diseases on mollusc populations may be mediated by a variety of factors, such as temperature increase, acidification, pollution, aquaculture and overfishing. Farmed and wild populations of molluscs are difficult to separate and therefore the presence of disease in one is likely to impact the other. Disease prevalence in wild and cultured conditions can differ considerably because of the different stresses that are likely to occur. In aquaculture, overcrowding can increase susceptibility to disease compared to the more dispersed wild populations. More research is necessary for biosecurity and protection of valuable marine food resources for a growing human population.