Since 1991, the number of penaeid shrimp occurring in Virginia waters of Chesapeake Bay has steadily increased, prompting an interest in developing a fishery. Although development of a shrimp fishery in the Chesapeake Bay region could bring economic benefits, the fishery may be hampered by the presence of a disease syndrome known as shrimp black gill (sBG). The objectives of our study were to (1) describe the spatial distribution and abundance patterns of shrimp in Chesapeake Bay, (2) relate relative abundance of shrimp to habitat characteristics, and (3) determine the presence and seasonality of sBG to better understand disease dynamics in the region. Subadult penaeid shrimp were collected monthly from Virginia waters by trawl from 1991 to 2017, and individuals were identified to species and counted. White shrimp Litopenaeus setiferus were the most numerous species captured, followed by brown shrimp Farfantepenaeus aztecus and pink shrimp F. duorarum. Shrimp were captured primarily from July to December. White shrimp were the only species that exhibited visible signs of sBG, which was first observed in October 2016 (13.4% prevalence); the condition continued into November and recurred the following year. Shrimp with visible signs of gill disease were examined by microscopy, histology, and PCR assay and were diagnosed with infections of a histophagous apostome ciliate, presumably Hyalophysa lynni. Any impacts of sBG on shrimp survival or marketability should be considered in fishery management plans to ensure sustainability of the resource