This study investigates the effects of seed dispersal through the European nutcracker (Nucifraga caryocatactes) on the genetic structure of Swiss stone pine (Pinus cembra). The corvid bird deposits several thousands of stone pine seeds annually in the soil as a future food resource. Since not all caches are recovered, this bird behaviour often leads to the establishment of Swiss stone pine seedlings. The combination of wind pollination with this bird-mediated seed dispersal can be expected to greatly shape the spatial distribution of genotypes and the genetic diversity within and among Swiss stone pine populations. Hence, the aim of this study was to investigate gene flow patterns, together with their effects on spatial genetic structure (SGS) and, thus, inbreeding probabilities in an exemplary P. cembra population. Furthermore, potential effects of inbreeding on offspring fitness were analysed, hypothesizing that rates of inbreeding and subsequent cumulative inbreeding depression are higher in small and patchily distributed than in large and continuous P. cembra populations. Molecular genetic results from the study population Rautialp show that both pollen and seed dispersal occur across the entire stand, supporting the assumption of extensive gene flow through far-ranging vectors like wind and birds. Nevertheless, we also found strong spatial autocorrelation of individuals within the population. This suggests that seed dispersal through nutcrackers occurs in a kin-structured manner, which leads to the establishment of SGS – especially in areas where tree density is low and seed shadows overlap less than in dense areas of the stand. The second part of the study shows that inbreeding rates were higher in small and peripheral than in large and continuous P. cembra populations, causing a reduction in offspring fitness. Taken together, this study suggests that small and isolated Swiss stone pine populations might be especially vulnerable to ongoing and future environmental changes.