Recent genetic studies, using maternally inherited mitochondrial DNA, indicate a complex evolutionary history for baboons Papio spp. in general, and for eastern African baboons in particular. To further address this topic and to improve our understanding of phylogeographic patterns of baboons in eastern Africa, mitochondrial cytochrome b sequence data were analysed from 148 baboon samples from 103 locations in eastern Africa. The resultant phylogenetic reconstructions suggest an initial split of baboons into four main clades: southern chacma baboons, baboons from Mahale Mountains in Tanzania, main southern, and main northern. We confirm that the boundary between southern and northern clades lies along the Ugalla-Malagarasi River and Ruaha-Rufiji River of central Tanzania. We detected new mitochondrial haplogroups, most notably the Mahale Mountains clade, and refined haplogroup distributions. The evolutionary divergence of baboons in eastern Africa was most likely triggered and maintained by numerous episodes of population division and reconnection, probably related mainly to climate change. To better understand these processes, nuclear DNA information is required, especially to assess gene flow among populations.