Both historical and contemporary processes can influence population genetic structure and phylogeographic patterns at different spatial scales. We studied the genetic structure of a common alpine caddisfly, Allogamus uncatus, across the central European Alps using mitochondrial cytochrome oxidase c subunit I (COI) sequence data to evaluate broad- and fine-scale spatial patterns in population genetic structure and examined how these patterns relate to historical and contemporary landscape processes. Both historical and contemporary influences on population genetic structure could be distinguished. At the broad-scale, our results showed the existence of 6 geographically structured haplogroups across the central Alps that were derived from 4 deeply diverged (up to 5.5%) older lineages. This broad-scale pattern in genetic structure of A. uncatus probably was the result of recolonization from multiple glacial refugia peripheral to the Alps. These data support the idea that phylogeographic patterns involving multiple refugia might be more common among alpine insects than previously thought. Within haplogroups, a finer-scale genetic structuring was found at the valley scale. Thirty of the 34 haplotypes found occurred in single valleys, demonstrating a high level of endemism and indicating little contemporary gene flow between valleys. This pattern might be typical for alpine specialists and other montane species with disjunct distributions. We suggest that these different scales of population genetic structure of A. uncatus probably were influenced by the fact that the species is a cold-tolerant alpine specialist. Hence, historical differences in availability of glacial refugia should be considered in conservation programs directed to preserve genetic variation in montane aquatic species.