The genetic resources of the caatinga ecosystem are under intensive pressure, due to economical conditions of the inhabitants of the region, or due to pressure to establish productive activities. The goal of this work was to study the genetic variability distribution in the Brazilian Semi-Arid region for the tree species umburana-de-cheiro (Amburana cearensis (Fr. Allem.) A.C. Smith), aroeira ... [Show full abstract] (Myracrodruon urundeuva M. Allem.) and baraúna (Schinopsis brasiliensis Engl.), based on RADP marker, in order to suggest prospecting and preservation strategies of the genetic variability of these species. It was evaluated 29 individuals for umburana-de-cheiro, sampled in five different regions, and 52 individuals for aroeira and for barauna, sampled in 11 specific regions, with definition based on the Northeast Agroecological Zoning. It was adopted the multidimensional scaling (MDS), based on the Jaccard's dissimilarity coefficient matrix, for the clustering analyses. Taking in account the difficulty to sample individuals, it was suggested primary focus on the strategies to preserve, in an order of priority, umburana-de-cheiro, aroeira and bara-na. The results observed for the tree species indicated that the individuals presented differences according the sampling region, with clusters of individuals being arranged according the sampling region, and that the genetic variability was not found to be equally distributed among all Semi-Arid regions. Strategies should consider a large number of small sites for in situ preservation or sampling of a large number of individuals for ex situ conservation in a large number of different units of the Northeast Agroecological Zoning to preserve the genetic variability of the studied species.