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Prosopis flexuosa is an arboreal Leguminosae that grows in arid and semiarid temperate zones of Argentina, in the Monte eco-region. It is a promising native forest species for recovering arid and semiarid regions because it plays an important role in erosion control as well as in soil fertility. Furthermore, it provides diverse economical resources. The main challenge to the forestry sector is finding a balance between production and forest protection. For this purpose, it is necessary to gather information about genetic parameters. In this study, we measured the distribution of the variation of 14 quantitative traits in an experimental half-sib stand, where families are representative of hierarchically structured populations. We applied a multivariate extension of the classical Q (ST) -F (ST) neutrality test to determine the relative importance of drift versus selection in the distribution of genetic variability. We found strong evidence that different selective regimes act on different traits and that selection favors different optima in each sampling site. The selection to different optima is much stronger among than within provenances. This result helps explain the possible causes for the regional variation observed in P. flexuosa and to define the management units and the evolutionarily significant units for this species.