Molecular genetic markers may reveal informative patterns of population processes such as historical migration, which may substantiate inference on postglacial re-colonization inferred, e.g., from fossil records. Palynological records of Swiss stone pine (Pinus cembra) suggest that the species has re-colonized the central Alps from a southeastern Alpine refugium after the last glacial maximum. Such a migration pathway likely resulted in a gradual decrease in genetic diversity with increasing distance to the glacial refugium, owing to founder events at the leading range edge. The present distribution of P. cembra in Switzerland consists of two rather distinct ranges, namely the inner-alpine parts of the Grisons and Valais, respectively, and additional disjunct occurrences in the northern and southern periphery of the Alps as well as between the two main ranges. We screened chloroplast microsatellite loci on 39 Swiss P. cembra populations and show that the genetic structure detected was congruent with a common ancestry from a single glacial refugium, likely located at the (south-)eastern periphery of the Alps. In contrast, our data rejected the alternative hypothesis of a distinct genetic separation of the two main ranges of Swiss stone pine in Switzerland. We further show that low genetic diversity within and high differentiation among peripheral populations in the northern Alps as well as the genetic differentiation between core and peripheral populations reflect genetic drift as a consequence of colonization history and limited gene flow by pollen and seed.