Résumé : Hydrochory plays a key role in the maintenance, diversity and evolution of aquatic plants and has traditionally been thought to (i) decrease or erase patterns of isolation-by-distance, (ii) increase outbreeding, and (iii) result in a downstream increase of genetic diversity. These hypotheses, which are especially relevant in organisms with water-mediated fertilization and a high ability to disperse vegetatively, are tested here from fine-scale spatial analyses of genetic variation at both the haploid and diploid phases in the aquatic moss Rhynchostegium riparioides (Hedw.) Cardot. A substantial geographical partitioning of genetic variation was found at the scale of the river basin and indirect measures of dispersal point to an overall weaker dispersal ability of the moss diaspores than pollen or wind-dispersed seeds. These observations, as well as the high Fis observed at the diploid stage and the very close proximity of potential fathers of the heterozygous diploid genotypes, strongly challenge the hypothesis that water enhances sperm and diaspore-mediated gene flow. In R. riparioides, the severe dispersal limitations revealed by the spatial analyses of genetic structure suggest that shoot fragments rather than spores are involved in local dispersal, which is fully consistent with the low levels of genetic diversity observed within populations. Extremely limited routine dispersal by unspecialized vegetative diaspores, coupled with discrete episodes of local population extinctions and colonizations by spores, account for the absence of a downstream increase of genetic diversity. As a result, although spore-producing plants are typically seen as most efficient dispersers, and although streams are traditionally seen as dispersal corridors, severe limitations of clonal dispersal at the local scale and discrete opportunities of random spore dispersal and establishment among colonies, both explain why typical metapopulation processes also apply to aquatic mosses. © 2013 Elsevier B.V.