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We used phylogenetic and phylogeographical methods to infer relationships among African ground squirrels of the genus Xerus. Using Bayesian, maximum-parsimony, nested clade and coalescent analyses of cytochrome b sequences, we inferred interspecific relationships, evaluated the specific distinctness of Cape (Xerus inauris) and mountain (Xerus princeps) ground squirrels, and tested hypotheses for historical patterns of gene flow within X. inauris. The inferred phylogeny supports the hypothesized existence of an ’arid corridor’ from the Horn of Africa to the Cape region. Although doubts have been raised regarding the specific distinctness of X. inauris and X. princeps, our analyses show that each represents a distinct well-supported, monophyletic lineage. Xerus inauris includes three major clades, two of which are geographically restricted. The distributions of X. inauris populations are concordant with divergences within and disjunctions between other taxa, which have been interpreted as results of Plio-Pleistocene climate cycles. Nested clade analysis, coalescent analyses, and analyses of genetic structure support allopatric fragmentation as the cause of the deep divergences within this species.