Several studies have assessed the phylogeographic patterns of vertebrates in North Africa and Sahara–Sahel, but most of the phylogeographic knowledge on amphibians comes from the Mediterranean region while the southern Sahara and Sahel remain poorly studied. Here, we assess the phylogeography of the African Groove crowned frog Hoplobatrachus occipitalis, with a focus on western Sahel in order to better understand the biogeographic patterns of semi‐aquatic species in this arid region. Using mitochondrial and nuclear markers, we have assessed the species’ genetic structure, distribution of genetic diversity, and the presence of cryptic diversity. We found evidence of a recent (re‐)colonization of the mountains in its northernmost distribution, but also for the role of southern Mauritanian mountains and large rivers as refugia. Two major lineages were detected, one perhaps endemic to Mauritania and the other widespread in Africa. The first lineage possibly constitutes the second Sahelian amphibian endemic; the latter may have originated through an allopolyploidy event, with the Mauritanian lineage being one of the parental ones.