The Franconian Alb (Bavaria, Germany) is rich in endemic Sorbus taxa, considered as apomictic microspecies and derived by hybridization between Sorbus aria aggregate and Sorbus torminalis (Sorbus latifolia aggregate). Molecular studies using the AFLP technique, neighbour joining, Bayesian clustering, principal coordinate analysis (PCo) and voucher studies were used to investigate genetic structure and origin of adult plants and cultivated offspring of three endemic S. latifolia taxa, namely Sorbus cordigastensis, Sorbus franconica and Sorbus adeana and probable parental species from the S. aria agg. and S. torminalis. The S. latifolia taxa, adults and progeny, showed low genetic variability and a more or less clonal structure, confirming an apomictic mode of reproduction. The investigated S. latifolia taxa were remarkably different among each other, confirming their status as microspecies. The AFLP data confirmed the hybrid origin of the S. latifolia taxa, they were 1.3–1.5 times more closely related to S. aria agg. than to S. torminalis. The S. aria agg. showed a complicate genetic structure and fell into four main groups, two intermediate groups besides Sorbus pannonica and Sorbus aria sensu stricto (S. aria s.str.). Some progeny of S. pannonica was more variable than expected and clustered partly with other groups indicating gene flow within S. aria agg. Different subgroups of the S. aria aggregate may be parental for the S. latifolia taxa, contributing to the remarkable genetic distances between them.