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Background  Hybridization of species with porous genomes can eventually lead to introgression via repeated backcrossing. The potential for introgression between species is reflected by the extent of segregation distortion in later generation hybrids. Here we studied a population of hybrids between  Salix purpurea  and  S. helvetica  that has emerged within the last 30 years on a glacier forefield in the European Alps due to secondary contact of the parental species. We used 5758 biallelic SNPs produced by RAD sequencing with the aim to ascertain the predominance of backcrosses (F 1  hybrid x parent) or F 2  hybrids (F 1  hybrid x F 1  hybrid) among hybrid offspring. Further, the SNPs were used to study segregation distortion in the second hybrid generation.    Results  The analyses in  structure  and NewHybrids revealed that the population consisted of parents and F 1  hybrids, whereas hybrid offspring consisted mainly of backcrosses to either parental species, but also some F 2  hybrids. Although there was a clear genetic differentiation between  S. purpurea  and  S. helvetica  (F ST  = 0.24), there was no significant segregation distortion in the backcrosses or the F 2  hybrids. Plant height of the backcrosses resembled the respective parental species, whereas F 2  hybrids were more similar to the subalpine  S. helvetica .    Conclusions  The co-occurrence of the parental species and the hybrids on the glacier forefield, the high frequency of backcrossing, and the low resistance to gene flow via backcrossing make a scenario of introgression in this young hybrid population highly likely, potentially leading to the transfer of adaptive traits. We further suggest that this willow hybrid population may serve as a model for the evolutionary processes initiated by recent global warming.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1552-6) contains supplementary material, which is available to authorized users.

RAD-seq reveals genetic structure of the F2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression