Striped bass, Morone saxatilis, is an economically and ecologically important species in the Chesapeake Bay and along the East coast of the United States. In 1997 an epizootic of mycobacterial infections was discovered in the Chesapeake Bay stock and subsequent reports indicated that up to three-fourths of subpopulations of striped bass in the Bay were infected, primarily older fish. This study investigated regional and age class differences in mycobacterial infections among younger striped bass in the Chesapeake Bay, and identified putative risk factors for infection. Approximately 2,000 0+ to 3+ age striped bass, a limited number of spawning stock, and bycatch species were evaluated for microbiology, histopathology and parasitology. Mycobacterial isolates were grouped according to gas chromatography fatty-acid methyl-ester profiles and multi-locus sequencing. Twenty-nine groups of mycobacteria were discerned including M. scrofulaceum, M. septicum, M. interjectum, M. triplex/M. montefiorense, M. szulgai, M. moriokaense, M. duvalii, M. avium, M. terrae, M. pseudoshottsii/M. marinum and M. shottsii, and several putative new species. The majority of mycobacteria groups observed had host overlap. Data revealed that prevalence of mycobacterial infection increased with age, up to 59%. Location of capture was associated with higher infection prevalence in fish sampled from the Pocomoke River compared with fish sampled from the Upper Bay (1+), the Choptank River (1+) and the Potomac River (0+, 1+). The presence of copepods, isopods, acanthacephalans, nematodes and trichodinid ciliates was associated with an increased prevalence odds ratio (POR) for mycobacterial infection, while the presence of bacteria other than mycobacteria was associated with a decreased POR for 0+ fish. Gender was not a risk factor for mycobacterial infection, however, gonads from some mature fish were infected. In addition, mycobacterial infections were observed in 12 other Chesapeake Bay fishes, including Atlantic menhaden, Brevoortia tyrannus, an important prey species. Mycobacterial infections in Chesapeake Bay fish appear to be more complex than the one pathogen-one host scenario. Further, vertical and food-borne transmission cannot be ruled out. Future research requires an holistic approach including evaluation of multiple host species in association with water quality and other environmental parameters.