Within and among population gene flow is a central aspect of the evolutionary history of ecosystems and essential for the potential for adaptive evolution of populations. We employed nuclear microsatellite markers to assess inter- and intra-population gene flow in five natural populations of Luehea divaricata growing in the Pampa biome, in southern Brazil. This species occurs in practically all secondary forests of the Pampa and has recognized ecological significance for these formations. The genetic structuring of the studied populations suggests limited gene dispersal among forest fragments, despite a homogeneous level of migration among populations. Notwithstanding the gene flow among populations, significant SGS is still found in some fragments. Significant spatial genetic structure within population was also found likely as result of limited seed and/or pollen dispersal. The scattered distribution of the populations and their relatively high density seem to limit pollen dispersal. Also seed dispersal by wind is not efficient due to large distances among forest formations. As conservationist actions towards preserving the genetic resources of L. divaricata and the Brazilian Pampa, we suggest the protection of the existing forest formations and the maintenance of the natural expansion of the forests over the grasslands in the biome.