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Numerous molecular studies emphasized how past climatic oscillations in the Sahara-Sahel have left strong imprints on current biodiversity patterns and identified the Atlantic coast and the Northwest African Mountains as refugia and speciation hotspots. Yet, the biodiversity inventory in the region is still far from complete. We use an integrative taxonomy framework to revise the systematics of the Mesalina olivieri species complex; integrating molecular, morphological, and environmental data, we evaluated levels of genetic and phenotypic differentiation among species/lineages and revised the species distribution limits of the M. olivieri complex, refining the distribution of Mesalina simoni, and Mesalina pasteuri. Our study confirmed one previously unidentified speciation event, leading to the description of Mesalina adrarensis sp. nov. Together with this new species, we also describe the south-western Moroccan populations of M. olivieri as Mesalina simoni saharae ssp. nov. Mesalina adrarensis sp. nov. is sympatric with M. pasteuri and parapatric with M. simoni saharae ssp. nov. in Mauritania and southern Morocco. Based on our revised taxonomy, M. simoni now includes most populations of the M. olivieri complex in Morocco, M. olivieri being restricted in Morocco to the east and southeast of the country. We also build on these results to provide further insight on the biogeography of North Africa. Our results point to a diversification of the complex during the late Miocene, that led to the formation of the four species M. simoni, M. olivieri, M. pasteuri, and M. adrarensis sp. nov. After these four speciation events, high intraspecific diversification processes occurred since the beginning of the Plio-Pleistocene transition, in parallel with the beginning of the humid and arid cycles. Through our phylogenetic analysis, we highlight the existence of high levels of undescribed intraspecific diversity in M. olivieri and M. pasteuri that will need to be addressed in future studies. Moreover, we uncover instances of cytonuclear discordances, stressing the need of considering both mitochondrial and nuclear DNA for integrative taxonomic studies to explore biodiversity.