The Pleistocene glaciations shaped the distribution and population structure of most European species. Some species survived the glacial cycles by shifting their range to Mediterranean refuges, while others endured in central European habitats. It has been argued that certain cold‐tolerant aquatic insect populations were able to persist in non‐freezing rivers close to glaciers. We aimed to identify the Pleistocene biogeographic history of a net‐winged midge (Blephariceridae), a relatively unknown group of Dipteran montane habitat specialists, by inference from its current population genetic structure. We sampled five mountain ranges covering the extent of the species range. We genotyped a novel set of 11 microsatellites and sequenced the mitochondrial cytochrome‐c‐oxidase subunit I region to detect genetic structure within and among five European mountain ranges in the net‐winged midge Liponeura cinerascens cinerascens. Liponeura cinerascens cinerascens shows distinct genetic differentiation between different mountain ranges, coupled, however, with near panmictic gene flow across distances exceeding 100 km within each studied mountain range. Distinct mitochondrial cytochrome‐c‐oxidase subunit I lineages with endemic haplotypes, microsatellite population genetic structure and high levels of regionally private alleles provide evidence that mountain range populations have been evolving independently from each other for a significant number of generations. Liponeura cinerascens cinerascens is able to maintain gene flow between watercourses in highly structured mountain ranges. Lowland regions, however, pose significant dispersal barriers, possibly because high‐gradient stretches with boulders are rare in such landscapes. We posit that each of the studied mountain regions represents an independent Pleistocene glacial refuge, and that L. c. cinerascens was able to persist glacial cycles in extra‐Mediterranean periglacial refugia in the Jura Mountains, Bavarian Forest, and Carpathians.