Riparian vegetation in temperate zones holds great environmental importance and thus its conservation should be a priority. Among riverine tree species, genus Populus stands out, being also a model organism in research. In this work, we present a genetic analysis of the hybrid Populus x canescens and its parent species Populus alba and Populus tremula, with special emphasis in P. alba with which backcrosses frequently occur. This study focuses on the river Douro basin (Spain) where the presence of hybrids has been previously reported. Nuclear microsatellite markers and Bayesian statistical analysis have been used for the detection of hybrids and purebred stands. This methodology has also made possible the study of clonality in the taxonomic continuum P. alba–P. x canescens. Our results highlight the existence of a small number of genotypes accounting for most of the individual trees and stands. Possible causes leading to this situation are discussed. Also, the presence of individuals genetically close to ornamental cultivars is reported for the first time. Finally, concern about the present situation of P. alba genetic resources is brought up.