The Scincidae represent about 26% of the known lizard species diversity. Although an abundance of literature exists, many unresolved taxonomic and nomenclatural problems remain in this group. 59 morphological characters and the mitochondrial genes 12S, 16S and cytochrome b were used to analyze the monophyly of 28 genera in Africa and to study the similarities and differences between African and Asian lygosomine skinks. My results show that two genera (Leptosiaphos and Eumeces) are paraphyletic. Moreover, the genus Panaspis seems to be constituted of two major lineages morphologically and genetically different, and we propose to re-validate the genus Paralygosoma for one of these lineages. My results show that African and Asian lygosomine skinks are genetically and morphologically different. Furthermore, African species of Lygosoma such as the African species Haackgreerius miopus are morphologically similar to the African genus Mochlus, thus I recommend placing them in the genus Mochlus.