Penaeid shrimp including Litopenaeus setiferus (white shrimp), Farfantepenaeus aztecus (brown shrimp), and Farfantepenaeus duorarum (pink shrimp) support one of the most valuable commercial fisheries in the U.S. Southeast Atlantic. Since the late 1990s, the fishery, especially in coastal Georgia and South Carolina, has experienced a significant decline. A contributing factor to this decline has been hypothesized to be a severe outbreak of shrimp black gill caused by a ciliate parasite. DNAsequence-based analysis of the gill parasite small subunit rRNA gene identifies the proposed causative agent as being closely related to the apostome ciliate Hyalophysa chattoni; however, morphological characteristics of the ciliate observed by electron microscopy are inconsistent with this identification. Although studies are ongoing to identify this ciliate, it was possible to develop a diagnostic polymerase chain reaction-based assay targeting the small subunit rRNA gene and use it to investigate the seasonal and geographic distribution of the parasite in wild shrimp populations. Next-generation sequencing of the gill microbiome confirmed that when black gill is at its peak, microeukaryotic communities were dominated by apostome-related ciliates, but over the year highly diverse communities of gill associates, including other potential ciliate, fungal, euglenozoid, and amoeboid parasites are commonly detected. Improved molecular diagnostics and the ability to explore the diversity of potential parasites in shrimp provide important new insights into the relationship between the shrimp fishery and black gill.