The dwarf bulrush (Typha minima Hoppe) is a perennial aquatic plant that has been rapidly disappearing in Northern Europe following flood control methods (dikes, dams, embankments). Floods, by erasing and creating new banks, maintain a metapopulation system (extinction/recolonization of populations). The largest and most diverse populations are located in France. To identify the size of the metapopulations, we studied clonality, genetic diversity and genetic structure of an extensive sample of the French populations using AFLP markers. Clonality was high (on average, each genotype was found in three copies) but variable across sites: some genotypes had a high number of copies (> 20) and were distributed over several river catchments while 239 genotypes were unique. Genetic diversity was high but did not accumulate downstream indicating both up- and downstream long-distance gene flow through pollen and seeds. Genetic diversity is structured in three major clusters. One (cluster N) is restricted to sites north of 44°4 N. The other two (clusters S and E), coexist in river catchments or even in the same site. However, the highest Fst were found between cluster E and clusters N or S, indicating a recolonization from different refugia, one possibly located east of the Alps (cluster E) and one or two on the Western side. Therefore conservation actions should take into account these three major conservation units (CU) in France. These CU cover large areas. It is thus important to maintain a natural river dynamics with frequent extinction/recolonization events over whole drainage basins.