Abstract Unidirectional hydrochory, reproduction mode and mating system have different impacts on the ecology of stream plants, and variation in the combination of these processes shapes unique genetic patterns which can have different consequences for the fitness of stream populations. We studied the genetic structure inferred by AFLPs, ITS SNPs and matK sequences of three populations of the common clonal macrophyte Ranunculus baudotii in River Aarhus in order to understand the role of vegetative and sexual reproduction in the stream and how genetic variation is distributed along the stream. We also explored the genetic relationships of the R. baudotii population in River Aarhus with other species of sect. Batrachium, because hybrids have been identified in the stream and they might affect the structure of the populations. The three studied populations were genetically distinct despite low genetic diversity and plant fragmentation is likely the main form of reproduction in the river system. The establishment of a few seeds, sexual recombination, the occurrence of putative hybrids and genetic drift in the establishment of fragments and seeds dramatically changed the genetic diversity of the populations along the stream and led to differentiation among populations. Further research is needed to understand the conditions favoring sexual reproduction and gene flow distances.

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