Abstract: Key message: Forest disturbance affects the within-population distribution of genetic diversity, but not its overall levels, in a tropical pioneer tree species. In particular, clumps of related saplings with impoverished diversity are found in canopy gaps but not under forest cover. Context: Forest disturbances can have long-term consequences on the genetic structure of tree populations, because they can alter the demographic properties of the regeneration process and favour some subpopulations/genotypes, both by stochastic processes and by selection. Intermediate disturbances tend to favour species diversity, at least in highly diverse communities, but their effect on intra-specific diversity is unknown. Aims: In this study, we have looked at the genetic consequences of forest disturbance in a stand of the long-lived Neotropical pioneer species, Jacaranda copaia. Methods: The study site was experimentally logged in 1984, and the canopy gaps generated by the logging were mapped. Seedlings of J. copaia colonised the gaps, as expected, at a higher density than in the surrounding forest. In 2006, we exhaustively sampled all saplings and adult trees available in a 25-ha area. The samples were genotyped at nine microsatellite loci, and the distribution of genetic diversity was inspected by analyses of spatial autocorrelation, automated Bayesian assignment and comparisons of diversity between cohorts by bootstrap (RaBoT). Results: Spatial autocorrelation was found to extend farther in post-disturbance saplings than in the undisturbed population (100 m and beyond versus less than 50 m), and divergent clumps (F<inf>ST</inf> = 0.05) of related genotypes were found; genetic diversity was found to be impoverished in each clump relative to the global population at about half of the loci. Conclusion: Overall, our results suggest that forest disturbance has changed the patterns of distribution of genetic diversity, with potential consequences on long-term population viability. © 2015, INRA and Springer-Verlag France.