The swim bladder inflates early after fish hatching via its interconnection with the digestive tract (ductus pneumaticus). This interconnection may serve as a portal to foreign particles, including bacteria, causing deficiencies in primary swim bladder inflation. We histologically examined 134 African annual killifish (genus Nothobranchius) with secondary loss of swim bladder function ('belly sliders'). We demonstrate that these fish lost the ability of air regulation in their swim bladders likely due to Mycobacterium spp. infection at an individual-specific age. Nearly all examined belly sliders had thickened swim bladder walls, and their swim bladder was filled with material containing mycobacteria, cell debris, young monocytic cells and phagocyting macrophages. Mycobacterial infection was restricted to the swim bladder in juveniles, where mycobacteria likely enter the host through the ductus pneumaticus. Infection in adults was systemic and mycobacteria were present in all examined organs. Presence of mycobacteria in the epithelial lining and submucosal layers of the digestive tract of adults suggests that it may also serve as the entrance site of infection. We suspect 2 sources of Mycobacterium contamination: dietary (with bloodworms) and/or contaminated hatching substrate. These sources of contamination may be eliminated by use of laboratory dry feed and egg disinfection prior to hatching.