The genetic variation in fourteen Sorbus torminalis (L.) Crantz. populations distributed over the eastern and south-eastern part of its range was studied using seven nuclear microsatellite loci. The differentiation level was relatively high (FST = 0.228), as expected for a species with a fragmented range. The distance-based approach to the analysis of differentiation patterns (neighbour-joining tree based on pairwise coefficients of differentiation) did not reveal a clear geographical structure. On the other hand, model-based Bayesian methods (BAPS and STRUCTURE) gave geographically continuous clusters of populations. The occurrence of populations deviating strongly from the general pattern is attributed to founder effect. In spite of a generally high differentiation, a significant isolation-by-distance pattern was found, which might be a consequence of postglacial migration and gene flow among descendants of different refugia.