Several diseases of fish present challenges to both fishery managers and aquaculturists in the Southeast. Emerging diseases along with a suite of known and persistent diseases can present management challenges for native species and biodiversity, can cause loss of recreational fishing opportunities, and can affect local economies or reduce profitability in commercial aquaculture. Emerging diseases such as mycobacteriosis in striped bass, epizootic ulcerative syndrome in menhaden, and spring viremia of carp present some new challenges to fishery managers. Likewise, recurring epizootics resulting from such etiologic agents as Streptococcus and Vibrio in estuarine fishes or Aeromonas and Edwardsiella in freshwater fishes have challenged managers for decades. Pathogens including Photobacterium damselae piscicida and several of the Mycobacterium species may represent health risks to managers, anglers, or fish culturists. Successful resource management depends on the ability of fishery managers to clearly understand the etiology of infectious diseases to both wild and hatchery stocks so that effective management and control strategies may be implemented. The needs for adaptive fisheries management strategies that employ fish health and disease considerations are discussed.