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Past climatic fluctuations have had a significant impact on the patterns of genetic variation within taxa restricted to montane regions and forested biomes; however, little is known about whether equivalent processes have occurred in arid biomes. Northwestern Namibia’s inselbergs provide a unique ecosystem in which to study the effects of major climatic events and geographical isolation on the genetic structuring of taxa in a subtropical arid biome. We investigated the phylogeographic structure of the black mongoose (Galerella nigrata), an inselberg habitat specialist endemic to this region, using mitochondrial DNA (mtDNA) haplotypes (cytochrome b, 1,089 base pairs) and nuclear microsatellite genotypes (15 loci) from 6 inselberg populations. Analyses of molecular variance and spatial analyses of molecular variance of the 14 mtDNA haplotypes identified 2 significant geographic barriers to the dispersal of black mongooses; these barriers occurred across the vast arid plains between Ruacana and Hobatere, and between Ohorongo and inselbergs to the south. The occurrence of mtDNA haplotypes that were restricted to specific populations also indicated some degree of isolation, likely resulting from limited gene flow and drift induced by the desertification of the landscape between inselbergs during the lead-up to the most recent glacial maxima. Despite this pattern of isolation, the widespread distribution of 1 mtDNA haplotype suggested that populations of black mongoose have, in general, been well connected in the past. Ongoing gene flow was further supported by Bayesian clustering of microsatellite genotypes, which showed 2 clusters, each spread across the mongoose’s distribution, and a lack of significant differentiation between populations. In addition, a constant population size was indicated by a Bayesian skyline plot. These analyses suggested that inselbergs across the entire study area might have supported black mongoose populations during some or all of the most recent major climatic fluctuations, with periods of isolation during glacial maxima and reestablished connectivity during interglacial periods.