We evaluated the amount and distribution of genetic variation in large and small isolated populations of Luma apiculata (DC.) Burret (Myrtaceae) in north-western Patagonia. The hypothesis tested was that isolated smaller populations were more affected by drift and isolation than large stands. Higher genetic diversity was predicted in the latter. Fresh leaf material for isozyme electrophoresis was collected from 30 individuals in four isolated and two large and continuous stands (Quetrihue Peninsula and Punta Norte, Isla Victoria). Five subpopulations were sampled in both large stands, and in addition, three regeneration gaps in Punta Norte. Eleven loci were resolved; 91% were polymorphic in at least one population. Isolated and large populations had similar levels of genetic variation. Reduced observed heterozygosity and elevated inbreeding were measured in subpopulations and regeneration gaps within dense stands. Although small populations consist of a reduced number of individuals they are mostly coastal populations nearby rivers and lakes that may maintain considerable gene flow with other faraway populations counteracting the effects of drift. In addition to potential selfing, increased inbreeding within large populations and regeneration gaps may be due to an intra-population Wahlund effect from local seedling establishment and vegetative spread, resulting in clustered cohorts of similar genotypes.