Species introductions have impacted the fishery potential, ecology and native fisheries populations of Lakes Victoria and Jipe. Oreochromis esculentus and Oreochromis niloticus have been widely introduced outside their native range establishing feral populations. However, the impacts of invasive species on management of native species biodiversity has not been documented. The establishment of exotic O. niloticus species populations in Lake Victoria has been accompanied by declining native populations of the O. esculentus and Oreochromis variabilis. These declines have been accelerated by the introduction of Nile perch, Lates niloticus, which preys upon the native O. esculentus, and overfishing of native fisheries which have slow growth rates and low fecundities. Moreover, nutrient pollution and eutrophication have impacted negatively the the food resources for native Singida tilapia O. esculentus. Native Jipe tilapia, Oreochromis jipe is limited in distribution to a small native range in the Pangani system comprising of Lake Jipe, the Pangani River tributaries and the downstream Nyumba ya Mungu Reseivoir. In Lake Jipe, two non-native species O. niloticus and O. esculentus have been introduced. Although the impact of O. niloticus on native O. jipe populations has not been documented, O. jipe has witnessed dwindling catches since the introduction of O. esculentus from the downstream reservoir. The decline can also be attributed to overfishing and the changing ecology of the lake after proliferation of emergent macrophytes such as Typha domingensis. There is need to formulate management policies to monitor and control fishing effort, pollution and protecting the lake and its catchment from degradation caused by human activities.