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Slavonian oaks (Quercus robur subsp. slavonica (Gáyer) Mátyás) originating from Croatia have been cultivated in Germany mainly in the Münsterland region of North Rhine-Westphalia since the second half of the nineteenth century. Compared to indigenous pedunculate oak stands in Germany, they are characterised by their late bud burst, but also by their excellent bole shape and faster height growth. Previously, Slavonian pedunculate oaks (= late flushing oaks) were mainly studied at chloroplast (cp) DNA markers in order to determine their geographical origin. The origin of the material is probably the Sava lowland between Zagreb and Belgrade. In the present study, the aim was to genetically differentiate between indigenous Quercus robur and Slavonian oak stands using nuclear DNA markers. For this purpose, we used 20 nuclear Simple Sequence Repeats (nSSRs). A total of 37 pedunculate oak stands (mean: 18.6 samples per population with an age of 95 to 210 years) were examined, of which 21 were characterized as Slavonian late flushing oaks and three stands for which the Slavonian origin was not clear. Maternally inherited chloroplast markers were analysed earlier in all 37 stands to validate their geographic origin. We found that the stands of native pedunculate oaks and Slavonian pedunculate oaks are represented by two genetic clusters which are weakly differentiated. Slavonian oaks (Na = 9.85, Ar = 8.689, Ho = 0.490, He = 0.540) showed similar levels of genetic variation as native oak stands (Na = 7.850, Ar = 7.846, Ho = 0.484, He = 0.526). Differences in growth and phenology and low but consistent genetic differentiation between groups suggest that both taxa represent different ecotypes with specific local adaptations, which are perhaps separated by less overlapping flowering phenologies. The nuclear microsatellite markers in combination with the cpDNA markers are suitable to differentiate between Slavonian and local oak stands. [ABSTRACT FROM AUTHOR]