Disturbance may generate population bottlenecks by reducing population size and the number of founders establishing a new colony. We tested the hypothesis that the scale of disturbance affects the levels of genetic diversity and the spatial distribution of genotypes in naturally regenerating stands of Nothofagus dombeyi, an evergreen angiosperm tree, in northwestern Patagonia. At similar spatial scales, we predicted that old-growth stands characterized by fine-scale gap phase dynamics would be genetically diverse due to restricted gene flow among temporal and spatially isolated gaps. In contrast, young massively regenerated postfire cohorts resulting from coarse-scale disturbances would be genetically more homogeneous. At each of three paired old-growth and postfire stands a minimum of 50 trees were mapped and sampled within 1 ha. Fresh tissue was collected for isozyme analysis from a total of 361 trees along with tree cores and diameters. Tree age distributions reflected the dominant modes of regeneration. Six out of nine analysed loci were polymorphic. Mean genetic diversity parameters were greater but not significant in mature stands. Fixation indices suggested significant heterozygous deficit at two-thirds of possible tests indicating a Wahlund effect due to local recruitment of related seeds. FST indicated moderate between-stand divergence. Mature stands concentrated half of positively like joins and yielded significant (P < 0.05) autocorrelation coefficients at small distance classes (< 20 m). Fine-scale patch dynamics within mature stands favours the maintenance of fine-scale genetic structure as a result of shade intolerance and local seed dispersal. Conversely, postfire stands suffer the effects of genetic drift given that a few reproductive trees produce a somewhat impoverished and genetically uniform progeny. Bottleneck effects will depend upon the density of remnant trees which could also be a function of the severity of fire.