Slavonian oak (Quercus robur subsp. slavonica (Gáyer) Mátyás) is currently gaining interest in forestry due to forest restructuring in Germany caused by climate change. Slavonian oaks originating from Croatia have been introduced into Germany mainly in the Münsterland region of North Rhine-Westphalia since the second half of the nineteenth century. They are characterized by their late bud burst, long clear bole, stem straightness and faster height and diameter growth compared to indigenous oaks in Germany. In this study, the genetic differentiation of adult trees and their respective progeny of two Slavonian and two indigenous stands in Hamm-Westtünnen, was evaluated. Genetic diversity and structure were estimated using 23 nuclear simple sequence repeat (SSRs) and 5 maternally inherited chloroplast microsatellite markers (cpSSRs). The mean expected heterozygosity of 0.545 and allelic richness of 6.23 indicate high genetic diversity in the studied populations. The group of progenies (AR = 8.40, Ho = 0.524, He = 0.559, FIS = 0.064) shows similar levels of genetic variation as the adult stands (AR = 8.37, Ho = 0.513, He = 0.554, FIS = 0.075). The genetic differentiation between adult stands and progeny was low (FST = 0.013). Genetic assignment of individuals using STRUCTURE revealed that the studied populations were divided into two clusters. There was no evidence of extensive hybridization or gene flow between Slavonian and native populations, possibly due to the different timing of bud burst of the two taxa.