The objective of this study was to assess the genetic diversity and dynamics in remnant patches of Araucaria angustifolia forest, with different levels of human modification. The Araucaria forest is one of the most important biomes occurring naturally in southern Brazil. Extensive logging and agricultural expansion in the last century resulted in significant fragmentation of the forest cover. Molecular genetic markers (microsatellite), combined with population genetics and landscape ecology, were used to improve the understanding of the impact of fragmentation on the forest and to develop guidelines for habitat conservation and restoration.