In this study, T and B lymphocytes were identified in the lungs of two potoroid marsupial species, the endangered Long-footed Potoroo (Potorous longipes) and the Long-nosed Potoroo (Potorous tridactylus). Using species cross-reactive antibodies, plasma cells, B cells and T cells were located in the alveolar septae and lymphocyte clusters were found adjacent to blood vessels and bronchioles. Bronchus-associated lymphoid tissue (BALT), resembling that of other mammals, was present within the bronchiolovascular bundles. Macrophages were occasionally visible in the alveoli, and areas of necrotic tissue in the Long-footed Potoroo contained collections of phagocytic cells, presumably macrophages, which contained acid-fast material and unidentifiable debris. This is the first report of BALT in Potoroo species and an important application of the only available antibodies that can reliably identify lymphocytes in marsupial species.