Aim Understanding the distribution and genetic structure of African mammals is key to reconstructing the continent's evolutionary history. While some parts of the continent (e.g., lowlands, mountain forests or savannah biomes) are now relatively well-studied, arid regions remain underexplored despite offering unique insights into adaptation to extreme environmental conditions. This study aimed to reconstruct phylogeographic patterns and past-to-future distributional dynamics of two gerbil genera-Pachyuromys and Desmodilliscus. Location North Africa, including the Sahara Desert and the Sahel. Taxon Two gerbil species from two sister monotypic genera: Pachyuromys duprasi Lataste, 1880 (Northern Sahara) and Desmodilliscus braueri von Wettstein, 1916 (Sahel region). Methods Using the most comprehensive available dataset, we examined mitochondrial markers (CYTB and COI) and built ecological niche models across past (Last Glacial Maximum, Mid-Holocene), present and future climate scenarios to investigate genetic structure and potential distributional shifts of both species. Results Desmodilliscus braueri exhibits a marked East-West phylogeographic structure, influenced by barriers such as the Niger River and Paleolake Chad. In contrast, Pachyuromys duprasi has genetically divergent populations in Egypt (which may be affected by a sampling gap in central-northern Sahara), but no broader spatial structure in its regions. Niche models suggest range contractions and expansions linked to climatic oscillations for both species. The predicted distribution of Pachyuromys reflects distribution area pulses, aligning with pulses in the extent of the Sahara. Main Conclusions Our findings emphasise the evolutionary significance of arid zones and the need for further research on species' responses to desertification and climate-driven range shifts. The contrasting patterns between the two species underscore different evolutionary trajectories in different taxa living in arid and semi-arid environments.