The Sorbus aria complex in the Franconian Jura, northern Bavaria, consists of the sexual diploid S. aria s. str. and putative apomictic polyploids, among them S. collina and S. danubialis. Here, the genetic and cytotypic structure of the S. aria complex and the proportion of clonal versus variable genotypes with a special focus on S. collina are studied using nuclear microsatellite markers, flow cytometry and multivariate morphometrics. In the Franconian Jura the tetraploid S. collina is the most frequent taxon in the S. aria complex. It consists of six closely related clones and a high number of unique genotypes, which were found in 70% of the populations studied. Morphologically, most of the clones and the unique tetraploid genotypes are not significantly differentiated. Therefore, all of them could be assigned to S. collina. Mechanisms that could result in the high number of genotypes within S. collina are accumulations of mutations, remnant sexuality, multiple polyploidization events and backcrossing. The results show that S. collina is a genetically quite variable facultative apomictic taxon. Triploids were identified sporadically and the microsatellites pointed to an origin from repeated hybridization events between diploid S. aria s. str. and S. collina.