Proliferative gill disease (PGD) caused by the myxozoan parasite Henneguya ictaluri is one of the most devastating parasitic infections in channel catfish aquaculture. Currently, there is no effective treatment for H. ictaluri and the unpredictable outbreaks can result in 100% mortality. Management strategies have been developed to prevent losses in newly stocked fingerlings by evaluating the PGD status of a pond prior to stocking, which is difficult since resident fish may not show clinical signs even when actinospore levels are lethal to naive fish. Current diagnostic methods are limited to the identification of an active infection and methods of predicting potential outbreaks have several limitations. The PGD status of a pond to be stocked can be determined using sentinel fish exposures which are labor intensive and require a source of parasite free fish. These limitations necessitated the development of more rapid and efficient means of determining actinospore concentrations to determine the risk of losing fish prior to stocking. The development of a quantitative real-time polymerase chain reaction (QPCR) assay provided a more rapid, sensitive and quantitative method of diagnosing active infections and also provides a means to predict potential PD outbreaks and determine the PGD status of a pond prior to stocking. Another approach in the control of this parasite is the identification of a less susceptible culturable species or to identify traits that could be targeted in a selective breeding program. Challenge studies have shown that the closely related blue catfish (Ictalurus furcatus) does not exhibit as severe an inflammatory response to H. ictaluri and mortalities are significantly lower than in channel catfish. Comparisons of PGD severity and H. ictaluri infection in channel catfish, blue catfish and channel x blue catfish backcross hybrids by gross examination, histopathology and the newly developed H. ictaluri real-time PCR (QPCR) assay supported previous research suggesting the life cycle of the parasite can not be completed as efficiently through the blue catfish host. This dissertation describes the development and validation of a QPCR assay to detect H. ictaluri in both fish tissues and environmental samples and the application of this assay in both research and production settings.