Oreochromis is the most important tropical freshwater fish genus for aquaculture purposes, with various introduction and translocation events having played an integral part of its management. Some Oreochromis species such as the Nile tilapia, O. niloticus, are thought to be superior for aquacultural purposes when compared to other species. Hence, understanding the admixed nature of the species within a native system is of key importance for the development of future broodstock. Using a combination of mitochondrial (COI) and nuclear (microsatellites) DNA, we tested for the presence of O. niloticus and O. leucostictus hybrids within the Lake Edward-George system. The present study revealed that, despite their natural overlapping ranges, hybridization between O. niloticus and O. leucostictus appears to be rare within the Lake Edward-George system, suggesting that the native populations of these two species may serve as suitable broodstock to develop future aquaculture strains. Moreover, our study provides the first COI sequences for O. leucostictus from its native range and adds to the growing database of O. niloticus sequences.