Lake Victoria and its basin are comprised of enormous areas of permanent and seasonal small water bodies that have been singled out as important faunal reservoirs for the endangered and threatened native species of Lake Victoria. Two tilapiine fish Oreochromis esculentus and O. variabilis are endemic and were the most commercial species in the lake fishery in early 1900s. Pressure on the fisheries and introduction of new fish species caused a severe decline of these species from the lake. However, almost all the native species that occurred in the main Lake Victoria have been encountered in satellite lakes within the lake basin. Fishery dependent surveys and experimental sampling using mono- and multi-filament gillnets were conducted between 2002 and 2014 in five lakes: Ikimba, Kalenge, Mitoma, Rushwa and Rwakajunju to determine and monitor distribution, population characteristics and relative abundances of the two species. The results showed the species still survive in these habitats but they are declining due to uncontrolled exploitation and environmental degradation. Threats to the survival of these species are outlined and recommendations on appropriate measures for conservation and sustainable management are suggested.