AbstractAimVarious species distributed in the Alps have their disjunct occurrences in the Carpathians. Fossil evidence for some woodland snails of Alpine distribution suggests that they colonized the Carpathians during the Holocene forest optimum or later. Here, we focus on disjunct Carpathian populations of the rock‐dwelling alpine snail Pyramidula saxatilis. As it occupies very stable habitats, that is, high‐elevation limestone rocks, one can assume its potential survival in Carpathian refugia over the glacial period(s). For comparison, the more widespread and warm‐climate P. pusilla is analysed.LocationEurope.TaxonPyramidula saxatilis and P. pusilla.MethodsWe analysed the genetic diversity of P. saxatilis and P. pusilla populations across their entire ranges using mitochondrial DNA and nuclear DNA markers. Seven fossil mollusc successions from the area where P. saxatilis occurs in the Carpathians were analysed and dated using the radiocarbon method. Habitat suitability models of both species were calculated for selected time periods since the Last Glacial Maximum.ResultsAll Carpathian P. saxatilis populations were genetically homogeneous and similar to those from the Eastern Alps. In P. pusilla, we found a genetically distinct lineage in the southern Western Carpathians. Both species were found in three fossil profiles since the Middle Holocene, and in one already in the Late Glacial. Habitat suitability models suggested the fluctuations of suitable conditions in the Carpathians driven by summer precipitation, especially for P. saxatilis.Main ConclusionsOur results suggest that the Carpathian populations of P. saxatilis represent a post‐LGM colonization from the Eastern Alps triggered by climatic changes, mainly by the increase in summer precipitation during the Late Glacial interstadials and Middle Holocene. The evidence for P. pusilla is similar, but also suggests rare long‐term survival in the Carpathian microrefugia. The palaeoecological evidence indicates a possible threat to high‐elevation species from future fluctuations in precipitation regimes.