The Tibagi River, located in southern Brazil, is associated with a significant degree of environmental heterogeneity, along its 550 km extension. There is concern about the integrity of this river’s ecosystem, as human interference has been increasing. Aegiphila sellowiana (Lamiaceae) is an important pioneer tree species, commonly found near rivers; the fruit is consumed by avifauna. We studied this species along three ecological gradients, comprising the upper, middle, and lower regions of the Tibagi River basin. The genetic structure of nine subpopulations of A.