1. Clonal herbs are an important feature of the understorey of Amazonian forests. However, little is known about the environmental drivers determining the population genetics of these herbs and about the spatial scale of gene flow.
2. With amplified fragment length polymorphism markers, we analysed the clonal diversity and genetic structure of a clonal Amazonian herb (Heliconia metallica) in south-eastern Peru at two spatial scales. First, we sampled leaves in 24 patches differing in flooding frequency and canopy openness in 2 km2 of a floodplain forest, and second in 21 riverine populations from the Andean foothills to the Amazon lowlands along a 550-km stretch of river.
3. At the small spatial scale in the floodplain forest, the clonal diversity of H. metallica was higher at flooded than at non-flooded sites, but clonal diversity did not increase with canopy openness.
4. At the large spatial scale, clonal diversity was very low in riverine populations at up- and downriver sites, suggesting that seedling recruitment was higher at mid-altitudes where the flooding intensity is intermediate. Genetic diversity of riverine populations monotonously increased downriver, indicating unidirectional gene flow mediated by hydrochory.
5. Genetic differentiation among riverine populations was very low (FST = 0.06) and followed an isolation-by-distance pattern, indicating a stepping-stone type of gene flow by seeds. Despite the much smaller spatial scale, genetic differentiation among patches in the floodplain forest was higher (FST = 0.16), due to spatially restricted gene flow in the forest understorey.
6.Synthesis. The genetic structure of H. metallica is the result of seedling recruitment being largely limited to flooded sites and of hydrochoric seed dispersal between populations growing on riverbanks. We conclude that river dynamics are the major determinant of the genetic structure of Amazonian plants and that largely undisturbed river systems, such as the Amazon, provide a crucial vector for gene flow, even at large spatial scales.