Aim General models for understanding the climate-driven processes of post-glacial colonization in European arctic–alpine species are mainly derived from studies on temperate terrestrial taxa. However, cold-adapted freshwater species may tolerate or even thrive under colder climatic conditions as flowing water habitats are thermally buffered against freezing and extremely cold tempera-tures. Here, we investigate the European Pleistocene and Holocene history of the arctic–alpine stonefly Arcynopteryx dichroa. Location Europe. Methods We used two genetic data sets (mitochondrial sequence data and nuclear microsatellite data) to investigate the glacial survival and post-glacial recolonization routes of A. dichroa. We used species distribution models to critically evaluate our genetic data and phylogeographical interpretations. Results Among 344 sequenced individuals from eight European mountain ranges, 80 unique haplotypes were detected. Of these, 77 haplotypes were ende-mic to a single mountain range, indicating almost complete lineage sorting. Both sequence and microsatellite data suggested strong population differentia-tion between mountain ranges. The genetic hotspots were found in the Carpa-thians, the Balkans and the eastern Alps. The Black Forest and Fennoscandian populations exhibited shared and closely related haplotypes, indicating ances-tral polymorphism in two populations that became disjunct due to vicariance or resulting from rare long-distance dispersal among disjunct northern and southern periglacial populations. Main conclusions Arcynopteryx dichroa is a glacial relict that survived glacial cycles through elevation shifts in isolated periglacial populations in the Pyre-nees, the central European highlands, the Carpathians, the Balkans and the eastern Alps. The species probably recolonized the formerly glaciated Fenno-scandian range from a refugium in the central European highlands, following the retreat of the ice sheet. This study suggests that aquatic organisms may have reacted differently to Pleistocene climate change compared with terrestrial species.