In this paper random amplified polymorphic DNA (RAPD) was used to evaluate the degree of among-population differentiation and associated spatial patterns of genetic divergence for Dipteryx alata Vogel populations from Cerrado region of central Brazil, furnishing support for future programs of conservation of this species. We analyzed patterns of genetic and spatial population structure using 45 RAPD loci scored for 309 trees, sampled from five different regions with two populations each. Genetic structure analysis suggested that panmixia null hypothesis can be rejected, with significant among-population components of 15%. Hierarchical partition by Analysis of Molecular Variance (AMOVA) shows that 5% of genetic variation is within regions, whereas 10% of variation is among regions, and these results were confirmed by a Bayesian analyses on HICKORY. The Mantel correlogram revealed that this divergence is spatially structured, so that local populations situated at short geographic distances could not be considered independent units for conservation and management. However, genetic discontinuities among populations were found in the northwest and southeast parts of the study area, corresponding to regions of recent socio-economic expansion and high population density, respectively. Taking both geographic distances and genetic discontinuities into account it is possible to establish a group of population to be conserved, covering most of D. alata geographic distribution and congruent with previously established priority areas for conservation in the Cerrado region.