Abstract• This study investigated the short-term changes in neutral genetic variation that would occur if a mature, second-growth, black walnut (Juglans nigra L.) stand was harvested following either a diameter-limited or value-limited cutting regime.• This research tested whether or not the neutral genetic variation within a natural stand of black walnut was disproportionately distributed within the larger or more valuable cohort of trees. To test this hypothesis a complete census of 278 trees from a black walnut stand in Indiana was genotyped using 12 highly polymorphic microsatellites.• Two types of simulated harvests were performed: (1) diameter-limit cuts, where every tree above a given diameter was removed; and (2) selective harvests based on value, where subsets of the most valuable trees were removed. Allelic diversity of the remaining population after each simulated harvest was compared to a corresponding distribution of outcomes from 10 000 random harvests of equal intensity.• None of the simulated harvests resulted in a reduction of allelic diversity significantly greater than that expected under random harvest, indicating that the allelic diversity of the population was evenly distributed across the entire population.• These results indicated that typical harvest scenarios do not per se lead to loss of allelic diversity among trees for this species.