Noccaea caerulescens (Brassicaceae) is a pseudometallophyte species occurring on normal soils, as well as on serpentine and calamine soils of natural and anthropogenic origins. The species is not only tolerant to cadmium (Cd), nickel (Ni) and zinc (Zn) but is also hyperaccumulator of these metals. Studies investigating the distribution of quantitative variation for these metal-related traits usually revealed that it was structured among populations according to edaphic types: calamine populations tolerate more and hyperaccumulate less Zn than non-metallicolous and serpentine ones; calamine populations from Southern France show the highest levels of Cd accumulation; serpentine populations tolerate and hyperaccumulate more Ni than other populations. This non-random distribution of quantitative variation suggests that microevolution of metal tolerance and hyperaccumulation is shape by the local adaptation to soil metal toxicity. However, apart from this ecogeographical knowledge, the ancestral relationships among populations are unknown. This lack of phylogeographic knowledge excludes any comparative synthesis of available phenotypic or molecular data. In particular, it prevents a comprehensive discussion about the possibility that local adaptation occurred several times independently and that underlying genetic mechanisms could vary among populations. To advance the understanding of among-population differences in metal hyperaccumulation and tolerance abilities, we studied the population genetics and demographic history of N. caerulescens in Western Europe. Sampling of seven to 30 plants was carried out in 62 sites. Genotyping was done using a combination of chloroplast and nuclear neutral markers. A strong genetic structure was detected, allowing the definition of three genetic subunits. Subunits showed a good geographical coherence. Accordingly, distant metallicolous populations generally belonged to distinct subunits. Approximate Bayesian Computation analysis of demographic scenarios among subunits further supported a primary isolation of populations from the Southern Massif Central prior to Last Glacial Maximum, whereas northern populations may have derived during postglacial recolonization events. Estimated divergence times among subunits were rather recent in comparison to the species history, but certainly predate the establishment of anthropogenic metalliferous sites. Our results suggest that the large scale genetic structure of N. caerulescens populations pre-existed to colonization of anthropogenic calamine sites. This suggests that local adaptation in distant polluted sites could have occurred independently, from distinct genetic backgrounds. However, admixture signals among distant metallicolous populations suggest human activities may have facilitated long-distance genetic exchanges. Finally, features of the most divergent genetic unit (e.g. extreme levels of Cd accumulation observed in previous studies) question the putative relationships between adaptive evolution of metal-related traits and subunits isolation.