River regulation results in the disconnection and increased fragmentation of habitats in the river corridor. In this study, we investigated the within-population genetic variability and among-population genetic differentiation of 21 populations of Origanum vulgare along the River Meuse, using dominant AFLP markers, in order to asses the restoration potential of this species in the context of current river restoration efforts. The average observed within-population genetic diversity was high and suggests that river regulation and associated fragmentation of the populations have not strongly affected genetic diversity. The genetic differentiation between populations was high (Phi(ST) = 0.24) and can be explained by founder effects, rather than by genetic drift in isolated populations. We also detected a pronounced hierarchic spatio-temporal structure in genetic variation. This structure can be related to the irregular patterns in the flow regime of the River Meuse. Large floods are the major vector of genetic structure, but geographic upstream proximity, probably mediated by small floods, also has an important effect on genetic structure. Three distinct groups of populations were observed, two of which could be related to the extreme flood events of the mid-nineties of last century. Assignment tests revealed occasional long-distance seed dispersal with extreme flood events and local colonisation with more regular floods. Our study species optimally took benefit of the opportunities offered by the river restoration programme, with a strong colonisation after floods, and illustrates the need for maintaining river dynamics to conserve and restore genetic diversity. (C) 2008 Elsevier Ltd. All rights reserved.