• age classes;
  • allozymes;
  • conservation genetics;
  • deforestation;
  • gene flow;
  • inbreeding

We explore the genetic structure and variability in autochorous Metrodorea nigra (Rutaceae) and anemochorous Astronium graveolens (Anacardiaceae), two species affected by deforestation in the Atlantic Forest of Brazil. The effects of deforestation and the depletion of the habitat within the remaining patches of forest are evaluated by comparing the variability between saplings and adults of each of these two species. The results indicate that the depletion of forest land and the deteriorating condition of the remaining fragments of forest may reduce the level of endogamous breeding in wind-dispersed species. In autochorous species, the fragmentation of forest land has less notable effects on genetic attributes, but pollen flow could be decreased as a result of the reduced number of insects flying between the forest remnants. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164, 326–336.