The biogeography and genetic structure of species endemic to the high elevation sky islands (tepuis) of the Guiana Shield in eastern and southern Venezuela and adjacent areas of Brazil and Guyana are poorly known. We investigated the phylogeography and population structure of the tepui brush finch (Atlapetes personatus) as an exemplar of that biota. Mitochondrial DNA sequences revealed three monophyletic clades that correspond to major morphological subspecies groups occurring in eastern, southern, and northwestern regions of the Pantepui. Differentiation among the clades accounted for 95% of the total genetic variance. DNA sequences from three nuclear loci also showed marked divergence among those three regions. Estimates of gene flow between regions and sampled populations were all less than one individual per generation. Consequently, these subspecies groups ought to be recognized as species-level taxa. The results suggest there is more large-scale biogeographic structure within the Pantepui region than generally recognized. Additionally, within two of the three regions, genetic variance among tepuis was substantial at both mitochondrial and nuclear loci. Many of the sampled populations appear to be genetically independent units that are nearly cryptic morphologically. The sampled tepuis may be islands of habitat for this taxon and for conservation purposes.