Morphological variation between two wild populations of Nile tilapia Oreochromis niloticus from Lake Kivu and Ruzizi River respectively and a breeding strain (Nyakabera strain) of the same species was studied by a multivariate analysis of 21 morphometric characters and 4 meristic characters. Principal component analysis and cluster analysis of morphometric characters showed divergence between populations/strains while the same approach with meristic traits didn’t show discrimination between them. These results show that based on the morphometric traits, the two populations of Lake Kivu and Ruzizi River are close to each other and stand out from the Nyakabera strain. The morphological differences thus noted could be due to environmental factors or genetic differences or both combined, in relation to the geography and the life history of these O. niloticus populations considered.