Global climate fluctuated considerably throughout the Pliocene-Pleistocene period, influencing the evolutionary history of a wide array of species. Using the phylogeographic patterns within the hartebeest (Alcelaphus buselaphus (Pallas, 1766)) complex, we evaluated the evolutionary consequences of such environmental change for a typical large mammal ranging on the African savannah. Our results, as generated from two mitochondrial DNA markers (the D-loop and cytochrome b), suggest an origin of the hartebeest in eastern Africa from where the species has colonized other parts of the continent. Phylogenetic analyses revealed an early diversification into southern and northern hartebeest lineages, an event that may be related to the formation of the Rift Valley lakes. The northern lineage has further diverged into eastern and western lineages, most probably as a result of the expanding central African rainforest belt and subsequent contraction of savannah habitats during a period of global warming. The diversification events appear to have coincided with major climatic changes and are highly correlated in time. These observations strongly suggest that large-scale climatic fluctuations have been a major determinant for the species' evolutionary history and that hartebeest evolution has mainly taken place in isolated yet environmentally favourable refugia during periods of global warming. Indications of sudden population expansion for two putative ancestral hartebeest populations provide further support for a refugia-based explanation of the diversification events. Reciprocal monophyly between southern and northern lineages may suggest that reproductive barriers exist and that the hartebeest complex comprises two different species.