The rock-dwelling land snail Pyramidula pusilla was analysed genetically and morphologically with an emphasis on its eastern Alpine distributional area. Genetic variation and phylogeographic patterns were inferred by mitochondrial cytochrome c oxidase subunit 1 gene sequences (650 bp), while shell variability was investigated by shell measurements and landmark analyses. The phylogenetic analyses revealed two clades in Austria (clades 3 and 4), of which one also contained individuals from Turkey. Other samples originating from the Balkan region (Albania, Greece) and Turkey were well separated in the tree, forming two distinct sister clades (clades 1 and 2). Concerning clades 3 and 4 there is no clear geographical pattern and both clades cooccur at several (11) sites; the same is true for clades 1 and 2. There are also morphological differences between clades: clades 1 and 2 differ from the other clades in size as well as shape, whereas clade 3 differs from clade 4 only in size. Considering all results combined, they imply that the samples analysed might actually represent more than one species and that, contrary to former assumptions, two species of Pyramidula may occur within the eastern Alps. However, comprehensive taxonomic conclusions cannot yet be drawn, for reasons connected with insufficiently justified species assignment: (1) high morphological variation within clades, (2) lack of clear diagnostic information in original descriptions, causing a lack of reliable distributional data and (3) lack of data over the whole distributional range of the genus. Analyses of ncDNA (e.g. microsatellites) to quantify the extent of gene flow, as well as breeding experiments between different clades, could help to clarify the delimitation of species. Despite these taxonomic uncertainties, the results provide insights on Pyramidula within the eastern Alpine region, suggesting that it survived the Pleistocene oscillations without dramatic bottlenecks and is capable of fast expansion to (re)populate formerly glaciated areas.