Abstract Aquaculture is the fastest growing segment of food production and is expected to supply a growing portion of animal protein for consumption by humans. Because industrial aquaculture developed only recently compared to industrial agriculture, its development occurred within the context of a growing environmental awareness and acknowledgement of environmental issues associated with industrial farming. As such, parasites and diseases have become one of the central criticisms of commercial aquaculture. This focus on parasites and diseases, however, has created a nexus of opportunities for research that has facilitated considerable scientific advances in the fields of parasitology and aquaculture. This paper reviews Myxobolus cerebralis, Lepeophtheirus salmonis, white spot syndrome virus, and assorted flatworms as select marquee aquaculture pathogens, summarizes the status of the diseases caused by each and their impacts on aquaculture, and highlights some of the significant contributions these pathogens have made to the science of parasitology and aquaculture.