Faustina faustina is a conchologically highly diverse forest gastropod with several morphological forms. It is a Carpathian species, but it also occurs in northern isolated localities, where it was probably introduced. We performed the first phylogeographic analysis of 22 populations, based on three molecular markers: COI, ITS-2, and 28S rRNA. Genetic data were complemented by paleo-distribution models of spatial occupancy during the Last Glacial Maximum to strengthen inferences of refugial areas. We discovered high genetic variability of COI sequences with p-distances between haplotypes ranged from 0.2 to 18.1% (6.3–16.6% between clades). For nuclear markers, a haplotype distribution pattern was revealed. Species distribution models indicated a few potential refugia in the Carpathians, with the most climatically stable and largest areas in the Southern Carpathians. In some climate scenarios, putative microrefugia were also predicted in the Western and Eastern Carpathians, and in the Apuseni Mts. Our results suggest the glacial in situ survival of F. faustina and its Holocene expansion in the Sudetes. Although our genetic data as well as shell phenotypes showed considerable variation within and between studied populations, the molecular species delimitation approaches still imply only one single species. Our study contributes to the understanding of the impact of processes on shaping contemporary population genetic structure and diversity in low-dispersal, forest species.