Understanding the processes that have given rise to polyploid hybrid taxa is central to our understanding of plant evolution. In this study, we use an array of genetic markers in a population analysis to elucidate the hybrid origins of the Arran whitebeams Sorbus arranensis and S. pseudofennica, two woody plant taxa endemic to the Isle of Arran, Scotland. It has been proposed that S. arranensis was derived by hybridization between S. aucuparia and S. rupicola, and that subsequent hybridization between S. arranensis and S. aucuparia gave rise to S. pseudofennica. Analyses of species-specific isozyme, nuclear intron and chloroplast DNA markers confirm the proposed origin of S. arranensis, and indicate that S. aucuparia was the female parent in the hybridization. Analysis of microsatellite markers suggests that there have been at least three origins of S. arranensis on Arran. Microsatellite markers also support the proposed hypothesis for the origin of S. pseudofennica, and indicate at least five hybrid origins of this taxon. In total, three multilocus genotypes of S. arranensis and eight of S. pseudofennica were detected on Arran and multilocus genotypic diversity levels Hg were 0.09 and 0.63, respectively. Genetic differentiation (thetaST) values based on multilocus genotypes are substantial (0.344 and 0.470 for S. arranensis and S. pseudofennica, respectively) implying limited seed flow among populations. These results indicate that the endemic Sorbus taxa on Arran are the products of multiple and ongoing evolutionary events. This information must be incorporated into management policies for their future conservation.