Spatial genetic structure (SGS) holds the key to understanding the role of clonality in hybrid persistence, but multilocus SGS in hybrid zones has rarely been quantified. Here, the aim was to fill this gap for natural hybrids between two diploid, ecologically divergent European tree species with mixed sexual/asexual reproduction, Populus alba and P. tremula. Nuclear microsatellites were used to quantify clonality, SGS, and historical gene dispersal distances in up to 407 trees from an extensive Central European hybrid zone including three subpopulation replicates. The focus was on P. x canescens and its backcross parent P. alba, as these two genotypic classes co-occur and interact directly. Sexual recombination in both taxa was more prominent than previously thought, but P. x canescens hybrids tended to build larger clones extending over larger areas than P. alba. The 3.4 times stronger SGS in the P. x canescens genet population was best explained by a combination of interspecific gene flow, assortative mating, and increased clonality in hybrids. Clonality potentially contributes to the maintenance of hybrid zones of P. alba and P. tremula in time and space. Both clonality and SGS need to be taken into account explicitly when designing population genomics studies of locus-specific effects in hybrid zones.