Black gill disease in food shrimp (Litopenaseus setiferus and Farfantepenaeus aztecus) has been implicated in the significant decline of the Georgia shrimping industry. The disease is caused by the shrimp’s innate immune response to infestation by Hyalophysa lynni ciliate. The immune response encysts the ciliate on the shrimp’s gills resulting in melanized nodules that reduce the shrimp’s ability to process oxygen. As a consequence, the shrimp suffer increased mortality due to oxygen stress and increased predation because of their reduced capacity to escape. Causes of the recent rise in black gill prevalence are unknown, however there appears to be strong seasonal and temperature components to infection rates. Infection first appears in August, and prevalence increases through the early fall until dissipating in January with the cooling water temperatures. Additionally, food shrimp appear to contract the infection while migrating into the estuary to mature, rather than transporting the infection with them from the open ocean. My research will focus on answering some of the many questions surrounding this important parasite, including addressing sources of variation of transmission and developing models for evaluating mitigation methods to protect Georgia’s shrimping industry.