The taxonomic status of the gerbil Gerbillus amoenus in relation to Gerbillus nanus and the distribution range of these two species in Africa and/or Asia have long been debated and are not yet fully clarified. In our study, we identify two specimens of small gerbils that we captured in two localities of the south of Morocco, using morphometric and/or molecular tools. The body and skull measurements were not able to unambiguously discriminate between three closely related small gerbils (Gerbillus amoenus, Gerbillus nanus and Gerbillus henleyi). However, the cytochrome b gene analysis showed that our two specimens cluster unambiguously with haplotypes of G. amoenus. This represents the first genetic characterization of G. amoenus in Morocco. It confirms, based on mitochondrial DNA, that the previously described species living in Africa is indeed G. amoenus and not G. nanus, the latter species being present strictly in Asia.