Peripheral populations may be crucial for understanding processes underlying adaptive genetic variation. Their evolution and ecology are driven by various genetic and demographic processes, such as selection, gene flow and bottleneck. Peripheral populations often experience a reduction in density resulting in the Allee effect. The presence of interfertile species increases the opportunity for hybridisation, which allows for a rescue from the Allee effect, but at the risk of genetic extinction through introgression. In this article we investigated a peripheral population of Quercus pubescens, a European tree species. The study population is located in Poland, several hundred kilometres northwards from the main species range. Due to geographic separation, the study population exists under strong pressure of introgression from potentially inter-fertile Q. petraea and Q. robur, which are the only common oaks in Poland. The intermediate morphology between typical Q. pubescens and a common oak species found in the study population supports the introgression hypothesis, which could be in line with the earlier studies of this species complex conducted in the main range of Q. pubescens. Alternatively, the intermediate morphology could reflect the founder effect or selection at an ecological extreme. We attempted to verify these hypotheses using microsatellites and a reference of common oak species. The results showed that the study population is genetically distinct from both Q. petraea and Q. robur. Additionally, the population is characterised by a low effective population size and limited gene dispersal. This suggests that the study population reveals strong reproductive isolation from common species, implying alternative sources of atypical morphology.