Two groups of subspecies of the door snail Charpentieria itala are distributed in a mosaic pattern in the Southern Alps. Some subspecies that morphologically resemble Charpentieria stenzii occur at exposed rocks at higher altitudes, whereas other subspecies live on more humid rocks at lower altitudes. This pattern can be explained by two alternative hypotheses. Either the stenzii-like or ‘stenzioid’ subspecies have a common origin and represent relicts of an early colonization wave that survived the ice ages in isolated mountain refuges within the Alps, or the geographically isolated stenzioid subspecies evolved through parallel adaptation of C. itala populations to life on exposed rocks. In this study, the first hypothesis could be supported by several lines of evidence. Analyses of amplified fragment length polymorphisms (AFLP) data indicated a common origin of the stenzioid subspecies of the Bergamasque Prealps and of the stenzioid subspecies of the Brescia and Garda Prealps, whereas an outlier analysis detected only few AFLP markers that might be under selection. High 16S rDNA distances between subspecies suggest that the divergence of the subspecies predates at least most of the glacials. The occurrences of the stenzioid subspecies are concentrated in mountain areas that were not glaciated during the Last Glacial Maximum. The genetic differentiation and the isolated distribution areas of the stenzioid subspecies indicate that they survived in five separate mountain refuges in the Bergamasque, Brescia and Garda Prealps. In addition, the clustering of the Charpentieria itala latestriata populations from different valleys indicates a low-altitude refuge.