The Nile tilapia (Oreochromis niloticus) is the second-most economically important fish species in East African countries (EAC), surpassed only by the Nile perch (Lates niloticus). It is the most-farmed freshwater fish species in EAC and the second-most-farmed worldwide. Currently, in EAC, through direct stocking activities and likely indirectly via aquaculture escapees, Nile tilapia are present in waterbodies where it is not native and where it is thought to have contributed to the fish biodiversity loss observed in recent decades. Introduced Nile tilapia may hybridise with native, congeneric species, promoting genetic introgression that can be detrimental to the sustainability of biodiversity. Moreover, the translocation dynamics and escapes from aquaculture can contribute to artificial geneflow between Nile tilapia stocks, compromising their gene pool and the sustainability of the species as a fishery resource. In the current work, we review some examples of these phenomena in EAC. Additionally, we explore the importance of collecting genetic data to define baseline knowledge for native and non-native Nile tilapia populations that can be used in monitoring programmes for development, management and conservation of tilapia genetic resources.