In southeastern Brazil, the majority of the riparian ecosystems are fragmented and degraded mainly due to human activities. The perennial gymnosperm Podocarpus sellowii Klotzch is a typical tree species from a gallery forest in the rupestrian area. Ten alloenzymatic loci were used to estimate the allelic frequency of 232 individuals distributed in eight subpopulations naturally divided by rock outcrops. The results indicated high genetic variability for the species in all subpopulations, with HO varying from 0.593 to 0.658, and HE, from 0.484 to 0.502. No endogamy was observed within (f = -0.292) and for the population set (f = -0.264). Genetic divergence of the species between subpopulations was 2.1%. Historic gene flow was low between subpopulations located in different water streams, corroborating the positive and significant correlation between genetic and geographical distance (rm = 0.496, P = 0.022). Co-ancestry revealed that only population A presents continuous distribution of the genotypes up to 94 m. Sp statistics did not indicate significant spatial genetic structure in the populations. In all the subpopulations, values of effective sizes were higher than the numbers of sampled individuals. The balance between mutation and drift was not verified, indicating the occurrence of a recent population bottleneck. These data can be used to determine the most effective strategies for the genetic conservation of this species.