Previous genetic studies showing evidence of past demographic changes in African drosophilids suggested that these populations had strongly responded to Quaternary climate changes. We surveyed nine species of Zaprionus, a drosophilid genus mostly present in Africa, in forests located between southern Senegal and Gabon. The mitochondrial COI gene showed contrasted levels of sequence variation across species. Populations of the only cosmopolitan species of the genus, Z. indianus, and of its closely related sibling species, Z. africanus, are highly polymorphic and appear to have undergone a continuous population expansion beginning about 130,000years ago. Five less variable species probably underwent a population expansion beginning only about 20,000–30,000years ago. One of them, Z. taronus, was significantly structured between forest blocks. The last two species were nearly monomorphic, probably due to infection by Wolbachia. These results are similar to those obtained in three species from the melanogaster subgroup, and may be typical of the responses of African drosophilid populations to glacial cycles.