We used ecological information and current and historic species distribution models for the last glacial maximum (LGM) to develop hypotheses regarding the Pleistocene history of the montane, autumn-emerging caddisfly Chaetopterygopsis maclachlani. We used mitochondrial sequence data from the cytochrome oxidase I (mtCOI) gene of 282 specimens from populations across Europe to analyze the population structure and phylogeography of C. maclachlani and to test our hypotheses. We examined the population genetic structure with median-joining networks, analysis of molecular variance (AMOVA), exact tests of population differentiation, and Mantel tests of isolation by distance. Furthermore, we used tests for selective neutrality (Tajima's D, Fu's F_S) to infer potential population growth and expansion and Bayesian Skyline Plots to analyze past population dynamics. We found strong population structure with 47 different haplotypes that could be separated into a southeastern and a western clade. The western clade seems to have survived at least the LGM in an extra-Mediterranean refugium, independent of the southeastern clade. Within the 2 main clades, we found haplotype overlap between mountain ranges and a high proportion of private haplotypes (89%). As predicted for a montane species with very limited adult dispersal capabilities, many regions and populations are currently isolated and appear to be diversifying into independent lineages. We discuss speciation within the Chaetopterygini and the diversification of C. maclachlani in particular.