Microcystis aeruginosa is a toxic cyanobacterium, which is able to bloom in a wide range of freshwater ecosystems. By sequencing the Internal Transcribed Spacer (ITS) of the ribosomal operon, we compared the genetic composition of several French bloom-forming M. aeruginosa populations from two reservoirs located on the Loire River, at two sampling points located between these reservoirs, and finally in two ponds closely linked to this river. No significant difference was found in the genetic diversity of the six Microcystis populations but we evidenced a strong genetic differentiation between most of these populations. Indeed, the Microcystis population in the Grangent reservoir was genetically differentiated from the other three populations sampled further downstream, implying that no massive transfer of population occurs from this reservoir to downstream segments. We also found genetic differentiation between the populations from the two ponds, and between these populations and those from the Loire River. On the other hand, the same dominant genotype was found in the populations sampled both in the river and in the Villerest reservoir, suggesting the selection of a distinct genotype adapted to river conditions and also an accumulation of this genotype in the downstream reservoir. Finally, by comparing our ITS sequences with those available in the GenBank, no biogeographical differentiation could be detected at a global scale, suggesting that most of the Microcystis genotypes seem to be ubiquitous.