The impressive organismal diversity in the southern Appalachian Mountains can be attributed to processes of in-situ diversification but also to the mountains' nature as a refugium allowing lineage persistence since pre-Pleistocene times. But it is still unclear how much diversity can be explained by each process, especially among lesser-known groups like arthropods. Stenus, an extremely successful genus of rove beetles, has >3100 described species around the World, with approximately 50 of them present in southeastern North America. We study the relationships, diversity, distributions, and biogeographic patterns of the Appalachian Stenus fauna, analyzing new COI data for 149 specimens, most of them representing flightless, high elevation endemics, together with previously published sequences. We performed species delimitation analysis (ASAP) and generated phylogenetic hypotheses using Maximum Likelihood and Bayesian inference, including a time-calibrated phylogeny with substitution rates estimated with reference to the fossil record. Stenus specimens from Appalachia do not form a monophyletic group – all flightless species fall into two principal clades, neither closely related to winged species in the region. One, the ‘appalachianus lineage’, consists of species lacking abdominal paratergites, with an age of origin estimated in the Pliocene. Another, the ‘appalachimontium lineage’, comprises numerous species with distinct abdominal paratergites and an estimated age around the Mio-Pliocene boundary. Based on morphology we recognized 16 high Appalachian Stenus species in our sample, while ASAP results suggested 14. COI data suggest the existence of morphologically cryptic species not yet described. Most species-level lineages date to 1.5-3 Ma; however, some clear speciation events date to only ∼1Ma. Observed intraspecific diversity originated mostly within the past million years. High Appalachian species represent multiple, overlapping radiations. Speciation events were not, however, entirely synchronic. Major lineages are separated by the Asheville Depression, and most groups show a marked geographic structure.