* Thlaspi caerulescens (Brassicaceae) is a promising plant model with which to study heavy metal hyperaccumulation. Population genetics studies are necessary for a better understanding of its history, which will be useful for further genomic studies on the evolution of heavy metal hyperaccumulation. * The genetic structure of 24 natural Swiss locations was investigated using nuclear and plastid loci. Population genetics parameters were estimated and genetic pools were identified using Bayesian inference on eight putatively neutral nuclear loci. Finally, the effect of cadmium (Cd) and zinc (Zn) soil concentrations on genetic differentiation at loci located in genes putatively involved in heavy metal responses was examined using partial Mantel tests in Jura, western Switzerland. * Four main genetic clusters were recognized based on nuclear and plastid loci, which gave mostly congruent signals. In Jura, genetic differentiation linked to heavy metal concentrations in soil was shown at some candidate loci, particularly for genes encoding metal transporters. This suggests that natural selection limits gene flow between metalliferous and nonmetalliferous locations at such loci. * Strong historical factors explain the present genetic structure of Swiss T. caerulescens populations, which has to be considered in studies testing for relationships between environmental and genetic variations. Linking of genetic differentiation at candidate genes with soil characteristics offers new perspectives in the study of heavy metal hyperaccumulation.