Abstract. Dipteryx alata (Fabaceae) is a threatened tropical tree of the Brazilian Savanna. Due to deforestation of its biome, many individuals and populations are now spatially isolated in forest fragments, pastures, and along roads. Plans for in situ and ex situ conservation of the species are urgently needed. To support conservation, the mating system and pollen dispersal patterns must be better understood as they determine the levels of genetic diversity, inbreeding, and effective size of seed generations. Microsatellites were used to investigate the mating system, pollen dispersal, genetic diversity and spatial genetic structure (SGS), in isolated trees in pastures and along roads from two populations with different densities in the Brazilian Savanna. Our aim is to determine the potential of these trees to contribute to seed collection for genetic conservation. We found that the species presents a mixed mating system, strong individual variation in outcrossing rate (0.01-1.0), and non-random mating. Low population density resulted in lower levels of outcrossing (t m = 0.45) and mating among relatives (t m -t s = 0.12), but longer pollen dispersal distances (δ = 6,572 m) than in the higher density populations (t m = 0.90, t m -t s = 0.26, δ = 1,395 m). Mating among relatives was explained by SGS detected in the populations, associated with near-neighbor pollinator foraging behavior. Correlated mating indicates that a low effective number of pollen donors (1.5-10.3) fertilized the trees. Thus, open-pollinated seedling families present mixtures of different levels of relatedness and inbreeding. Our results are discussed in light of strategies for in and ex situ conservation.