Pectoral fin loss is a dramatic evolutionary phenomenon that has occurred independently in different teleost lineages. Here, we report the first case of pectoral fin loss in the Mastacembelidae (Teleostei: Synbranchiformes), with the discovery of a new species of mastacembelid from Lake Tanganyika (LT), Mastacembelus apectoralis sp. nov. M. apectoralis can be distinguished from all other mastacembelid species by its complete loss of pectoral-fin rays, distal pectoral radials and pectoral radials, as well as a reduction in pectoral girdle elements that include smaller and less well-developed coracoid and minute scapular bones. Other distinguishing characteristics include a near absence of scales, lack of pigmentation and the presence of well-developed adductor muscles. A previous multigene phylogeny of mastacembelids placed M. apectoralis sp. nov. within the LT species flock, having diverged from its sister species Mastacembelus micropectus∼4.5 million years ago. M. micropectus also shows a reduction in the size of its pectoral fin and endoskeletal girdle, and has largely cartilaginous pectoral radials and a reduced number of pectoral-fin rays. Here, we compare the pectoral girdle of M. apectoralis and M. micropectus with LT and non-LT African mastacembelids. M. apectoralis is currently only known from its type locality, Cape Kachese, Zambia, where it occurs in sympatry with several other LT mastacembelids, including its sister species M. micropectus. The loss and reduction of pectoral fins and associated girdle elements in M. apectoralis represents another independent occurrence of this evolutionary phenomenon within the teleosts. The discovery of this species highlights the exceptional diversity of this biodiversity hotspot, the understanding of which is of critical importance with the pressures of pollution, overfishing and climate change threatening the speciose and evolutionarily significant diversity of this ancient lake.