The status of African populations of farmed tilapia is reviewed and discussed in light of the need for improved strains for commercial aquaculture. Many tilapia populations currently held on African fish farms have been genetically compromised through one or more of the following: inbreeding, negative selection, genetic drift, and unregulated hybridization. Their performance is currently 20–40% lower than the wild populations with which they have been compared and almost 100% less than some improved lines. Basic genetic management through the use of rotational mating could at least maintain genetic integrity, whereas selective breeding has the potential to further improve performance. Environmental concerns over the use of improved stocks are based largely on case studies from Atlantic salmon aquaculture and might not accurately reflect the situation of farmed tilapia in Africa. Nevertheless, international guidelines for the conduct of appropriate cost/benefit analyses should be followed when deciding whether to use improved tilapias or not.