Management of freshwater fishes in zoos and aquariums for conservation breeding is a key area where much can be achieved with limited facilities and a comparatively modest financial outlay. Some species now survive only in captivity following in situ threats such as habitat loss. Fortunately, short generation length and high fecundity mean that populations of freshwater fishes can be readily maintained in anticipation of ecosystem reinstatement and a reintroduction programme, where conditions are appropriate. However, diseases that occur in captive populations may constrain any species recovery programme. Conversely, any disease not previously found in the wild population should not be present in captive fishes when the animals are reintroduced to the wild. Mycobacteriosis has regularly been identified in episodes of morbidity and mortality in groups of Extinct in the Wild and other threatened freshwater fishes maintained for conservation breeding. It is, therefore, a common impediment to breeding and reintroduction programmes. For any programme to succeed, the issue of disease management needs to be addressed and solutions found to the challenges. An overview of the elements that must be considered when mycobacteriosis is detected in captive populations of threatened freshwater fishes and ways in which these can be managed in aquariums are discussed here.