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Aim: Isolation is expected to lead to negative impacts on populations due to a reduction in effective population size and gene flow, exacerbating the effects of genetic drift, which might be stronger in peripheral and fragmented populations. Fagus sylvatica (European beech) in southern Sweden presents a gradient of isolation towards the leading range edge of the species. We sought to determine the impact of long‐term isolation on genetic diversity and population genetic structure within populations of this species. Location: Samples were obtained from 14 sites towards the northern edge of the native range of beech in Sweden. Taxon: Fagaceae. Methods: Using historical sources, we obtained area‐ and distance‐based measures of isolation. We measured genetic diversity and structure by using nuclear microsatellite marker data, and performed parentage analysis to estimate external pollen‐mediated gene flow. We implemented a partial least squares regression to determine the effects of isolation on each of the genetic diversity estimators and the measures of external pollen‐mediated gene flow. Results: Long‐term isolation generally had a negative impact on genetic diversity, which is exacerbated over time, further affecting progeny and suggesting that isolated populations are subject to strong genetic drift, possibly due to the combination of founder events and persistent small population sizes. Bayesian cluster analysis revealed that isolation was also acting as a barrier to gene flow in the north‐eastern distribution of beech. Main conclusions: Isolation at the leading range edge of beech in Sweden has created gradients of contemporary gene flow within the species. The long‐term cumulative effects of isolation on this wind‐pollinated tree species and its negative impacts on genetic diversity and gene flow, could lead to inbreeding depression and higher extinction risk where populations remain small and isolated. [ABSTRACT FROM AUTHOR]