The Sub-Saharan Great Lakes Region has a rich ichthyofauna most notably, the cichlids. Among the cichlids, the most important and commercially exploited are the tilapine species of which O. niloticus Linn, 1758 (Nile tilapia) is the most common. This vital resource has been subjected to immense anthropogenic threats primarily through fish translocations, overfishing, habitat destruction, climate change, alien invasive aquatic weeds etc. Hereby, the broader aim of this thesis was to investigate the impact of anthropogenic activities on the evolutionary trajectory of the East African O. niloticus particularly in nonnative habitats following the aforementioned activities in the region. This was investigated using the hypothesis that anthropogenic activities might have altered the natural morphology and genetic structure of O. niloticus through admixture and introgression with the indigenous congeneric species. Geometric morphometrics and molecular genetic markers were used to delineate the cichlid in the region from different East African localities, covering low and high-altitude environments. Samples were collected from three locality types; farms, lakes with natural but non-native (introduced) fish and lakes with native (indigenous) fish. The farms and non-native localities were only limited to Uganda. Additionally, samples at the continental level were collected, including populations from the West African country of Burkina Faso and Ethiopia to test and compare the genetic structure with the East African ones. For morphometric analysis only the East African populations were included. During geometric morphometrics analysis, two thin plate spline (Tps) programs; Tps Utility (TpsUtil) and Tps digitizer (TpsDig) were utilized. These programs were used to acquire landmarks on fish digital photographs and henceforth generation of x, y coordinates which were then imported into MorphoJ program for subsequent multivariate analyses (chapter 2). At molecular level, 64 microsatellites (SSR) loci were developed and 26 were employed to test the four East African/Uganda populations. Here, the latest genotyping by sequencing approach using SSR loci (SSR-GBS) was compared with the traditional fragmented length analysis by assessing the information content recovered with the two approaches (Chapter 3). SSR-GBS was then applied in Chapter four to investigate all the sub-Saharan Nile tilapia populations. A total of 40 SSR loci were used for amplifying all the present studied populations. Geometric morphometric analysis generally revealed that all the East African populations were somewhat homogeneous in shape, implying close relation. However, when principle component scores (PC1 and PC2) were plotted against the axes, it was clear that the non-natives; Victoria and Kyoga, were morphologically divergent from for instance some native populations (Kazinga Channel and Edward). But the non-native Victoria and Kyoga appeared undifferentiated from some natives like Albert, George, River Nile and Turkana. The shape variation among the East African Nile tilapia populations was suspected