The West Sahara-Sahel is a remote region where knowledge gaps on mammal distribution have hampered accurate local biodiversity assessments and the development of optimised conservation planning in the region. Using a geographical information system and ecological niche-based modelling tools, this study combines high resolution presence data from 22 mammals and environmental factors from the West Sahara-Sahel to identify suitable areas for mammal occurrence, biogeographic affinities among taxa, and local hotspots of species richness. The maximum entropy approach was used to relate environmental factors with mammal distributions and to predict suitable areas of species’ occurrence. Biogeographic groups were defined based on the spatial similarities of predicted distributions. Ecological niches of analysed taxa were summarized through Principal Components Analyses based on topoclimatic and habitat variables. Distributions of most mammals were related with climate and/or habitat features, and some were associated with topography. Suitable areas were predicted mostly within known distributions of mammalian taxa. Low values of niche breadth were estimated for all taxa, indicating a tendency for specialization in the study area. Shared distributional ranges among taxa allowed the identification of five groups with different biogeographic affinities. Most groups occurred in the ecoregions North Saharan steppe and woodlands and Sahelian Acacia savanna, reflecting their availability and stressing the importance of these ecoregions for local mammal conservation. Predicted suitable areas were poorly represented in the current network of protected areas, especially in Mauritania. The southern Mauritanian mountains accumulated most of the studied mammals, but are largely unprotected. This study updated the current knowledge on the distribution and habitat selection patterns of the analysed mammals in the West Sahara-Sahel. The fine scale ecological niche-based models built with high resolution data can be used to identify key-areas for conservation and management, and could be applied to other remote regions and taxonomic groups worldwide.