Understanding the combined effects of multi-parasite infections on their hosts is necessary for documenting parasite impacts and is particularly important for developing effective management strategies for economically important organisms. The white shrimp Penaeus setiferus supports important recreational and commercial fisheries along the southeastern and Gulf coasts of the United States and occupies an important ecological niche in estuarine and offshore habitats throughout these regions. The goal of this study was to identify and assess ontogenetic and spatial variation in white shrimp parasite communities and their relation to shrimp health. We used a series of trawl surveys in tidal creek and open water habitats of an estuary in the southeastern USA to collect and identify parasites of white shrimp using morphological and DNA sequencing techniques. Parasite communities in white shrimp were composed of organisms belonging to 6 classes: Conoidasida (gregarines), Oligohymenophorea (apostome and sessilid ciliates), Microsporea (meiodihaplophasids), Chromadorea (rhabditids), Cestoda (cyclophyllideans, lecanocephalideans and trypanorhynchs) and Trematoda (plagiorchiids). Parasite communities differed significantly among white shrimp life stages and localities. Furthermore, the health condition known as black gill occurred in some shrimp and was significantly related to parasite community structure. Infection metrics for the apostome ciliate Hyalophysa lynni, the trypanorhynch larvae Prochristianella sp. and the rhabditid larvae Hysterothylacium sp. were significantly different between shrimp exhibiting and not exhibiting black gill. These results highlight the importance of understanding parasite communities and the potential interactive effects of multiple parasite infections on shrimp health.