The dataset contains individual genotypes at 11 nuclear microsatellite markers of samples of Swiss stone pine (Pinus cembra). Samples were collected in 12 natural and presumably planted stands in the canton of Fribourg (Switzerland). The dataset is complemented by individual genotypes (same markers) from samples of a subset of 40 populations across the European Alps (taken from Gugerli et al., Journal of Biogeography 2023; https://doi.org/10.1111/jbi.14586; dataset archived at Dryad, https://doi.org/10.5061/dryad.866t1g1v6).