Understanding of large-scale biodiversity patterns is fundamentally limited by gaps in knowledge of species taxonomy, distributions and evolutionary patterns. Here we propose rodents and shrews as taxonomic groups very suitable for deciphering factors that shaped biodiversity of Africa. Phylogenomic analyses will be used for (i) unbiased quantification of evolutionary diversity (e.g. re-evaluation of biodiversity hotspots, centres of endemism), (ii) parametrized description of its dynamics (e.g. diversification rates, cradles & museums of diversity), and (iii) synthetic biogeographical scenarios (e.g. evolutionary origins of biogeographic assemblages). The project builds on a considerable body of phylogenetic work done in the last decades, uniquely comprehensive sampling of material and sequence data, and close collaboration with teams working in other parts of Africa. The proposed approach will allow unparalleled analysis of biodiversity patterns and underlying processes at continental scale and might have important implications, e.g. in prioritizing areas for nature conservation.