The taxonomical complexities consistently challenge the continued use of the Tilapia as an aquaculture candidate. These complexities have been fueled by fish translocations leading to hybridization and admixture which complicate taxonomy and sound units for management and sustainability. Amidst these challenges, less information is available that is useful to fully understand the African Tilapiines at the continental level. This study characterized 10 tilapiine species collected from different water bodies in Africa, using microsatellites and mitochondrial markers. Three and two lineages of Oreochromis niloticus and Oreochromis esculentus respectively are defined. Among the 50 populations, comparisons among the East African water bodies showed extremely lower genetic differentiation. For example, Kyoga and Victoria (0.03), and Mulehe and Kayumbu (0.19). Multivariate analysis like principal coordinate analysis (PCoA) showed higher levels of admixtures between the natural and translocated populations. The high level of introgression was recorded between Oreochromis machrochir and Oreochromis mweruensis. These results provide valuable insights for biodiversity conservation, fisheries management, and the development of genetically sustainable Tilapia breeding programs, ensuring the long-term viability of these species in their natural habitats and aquaculture settings.