Aim: Phylogeographic studies on savanna ungulates have extensively evaluated genetic patterns mostly related to Pleistocene climatic oscillations. We address this subject through a comprehensive assessment across the pan-African range of the roan antelope, assessing whether climatic oscillations or natural physical barriers play a predominant role in the evolutionary history of the species. We also address the spatial concordance of the genetic structure with the currently recognized subspecies. Location: Sub-Saharan Africa. Taxon: Roan antelope (Hippotragus equinus). Methods: We genotyped 43 microsatellite loci and sequenced whole-mitochondrial genomes for 131 individuals across the species' entire African range. We performed spatial analyses of genetic diversity for contemporary and historical samples and calculated overall patterns of genetic differentiation and structure for both marker types. We also estimated the timing of divergence events and demographic trends, correlating these with the species’ biotic attributes as well as abiotic features shaping African savanna habitats. Results: Our analyses uncovered highly structured clusters and contact zones across the distribution of the roan antelope, including five nuclear groups and four mitochondrial lineages. The north-west group had the highest level of intra-group diversity as well as inter-group divergence and represents the oldest vicariant event. The central and southern groups had the lowest intra-group diversity with low divergence values separating them, suggesting a more recent ancestry for these groups. All population groups showed signals of demographic stability over time showed signals of demographic stability over a demographic decline during the Holocene. Main conclusions: The roan antelope exhibits significant population structure across its African range. This structure is largely associated with natural physical barriers, whereas contact zones could more easily be explained by climatic events. Based on estimates of genetic diversity, we propose a West African ancestry for this species with subsequent eastward and southern range expansions, as well as the persistence of stable population numbers within refugia. A general trend of population size decreases likely reflects Holocene extreme climatic events and increased human pressure.