The southern Appalachian Mountains in eastern North America host exceptional diversity, a substantial proportion of which has been generated in place. Yet, beyond broad generalities, bio- and phylogeographical patterns, and the temporal scale of diversification in the region are poorly resolved. Using one mitochondrial and one nuclear marker, we analyze intraspecific diversity patterns in a flightless, litter-inhabiting rove beetle Dasycerus carolinensis Horn. Our goals were to reconstruct the phylogeographical history of this species, producing a dated intraspecific phylogeny, and to examine previous hypotheses of possible cryptic divergence across populations of the species. Samples derive from a mix of old-growth fragments and secondary growth forests, and we also ask whether old-growth remnants host a larger proportion of genetic diversity in the species. We recover a strong primary subdivision among major lineages across the French Broad River basin (dated to ∼5.8 MYBP), and a secondary subdivision among western populations dating to ∼4.5 MYBP. Most interpopulation uncorrected divergences exceed 5%, strongly suggesting cryptic differentiation. Old-growth populations do not show greater genetic diversity than secondary-growth populations, indicating that most populations have persisted through recent anthropogenic disturbance.