Aim High mountain regions exhibit a much stronger environmental heterogeneity and a more complex glacial history than lowland regions. In this study, we compared the genetic variation of plant species occurring in different altitudinal zones. We tested the assumption that environmental and historic differences among high mountain regions and lowlands result in different patterns of genetic diversity and differentiation. Location Central Europe and the European Alps. Methods We first compiled a data set on genetic variation of 179 plant species occurring in Central Europe and the European Alps measured by AFLPs from the literature. Then, we compared genetic diversity and differentiation between species occurring in the lowland, montane, subalpine and alpine vegetation zone with the help of linear models. Geographic distance among sampled populations, plant frequency and three plant traits (life span, mating system and pollination mode) were included into the models, to account for their potential effects on level of genetic variation. Results Our analysis revealed different patterns of genetic variation in plant species occurring in the alpine and non-alpine zone. Genetic differentiation was significantly higher among populations of species from the alpine than subalpine, montane or lowland zone. In contrast, genetic diversity was significantly lower within populations from the alpine zone compared to the other zones. Main conclusions We argue that the observed pattern of genetic variation most likely results from restricted gene flow, both past and present, among spatially and environmentally isolated populations in alpine habitats.