The use of local provenances in restoration, agriculture and forestry has been identified and widely implemented as a measure for species and community conservation. In practice, provenances are often delineated based on climate, geomorphology and correlated spatial descriptors following the boundaries of larger natural regions. They are thought to comprise genetically homogenous plant material. Here we investigate genetic variation at AFLP loci in 26 natural populations of the regionally common grassland species Geranium pratense, which is often used in seed mixtures. Most studied populations are located in one previously delineated provenance in Germany. We assess within- and among provenance differentiation patterns and aspects of gene flow by investigating the mating system, the genetic structure at regional and local scale, gene dispersal and potential selective mechanisms that may have contributed to differentiation patterns found. Compared to other herbaceous, insect-pollinated grassland species and despite being outcrossed (mean t m = 0.88), G. pratense showed low genetic diversity (mean H E = 0.15), considerable genetic differentiation among populations within provenances (mean pairwise F ST = 0.20) and a pronounced within-population spatial genetic structure (mean Sp = 0.064). A genome scan approach identified three potentially adaptive loci. However, their allelic frequencies were only weakly related to climatic parameters thus providing little evidence for adaptive divergence. Nevertheless, the distribution of genetic diversity and derived gene dispersal estimates indicate limited dispersal ability, suggesting that gene flow at distances larger than 10 km is negligible. Our findings may question the approach of delineating provenances by general criteria, and highlight the importance of species-specific studies on differentiation and adaptation patterns.