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Ecosystem restoration has gained increasing interest to mitigate the effects of climate change, loss of biodiversity and desertification. Since the genetic composition of the reproductive material to revegetate degraded areas affects the success of restoration throughout time, information on the genetic properties of possible seed sources is essential to evaluate the risks associated to management practices. Prosopis flexuosa (Leguminosae) is an important native species in Argentina valuable from an economic and ecological point of view. Aiming to give restoration recommendations for the use of this species for rapid recuperation of the plant cover in arid regions of Monte desert, our goals were to quantify the genetic basis of phenotypic differences in height and basal diameter and the genetic differentiation of neutral markers among several provenances installed in a provenance and progeny test. Ours results suggest that the morphological variation have a significant genetic basis and differences among provenances may be explained by local adaptation. Low but significant genetic differentiation was detected by microsatellites among provenances. From our results the recommendation to provide a broad genetic basis in a restoration programme is obtaining seeds representing all genetic clusters identified, rather than all provenances. This implies avoiding sampling of more than one provenance embracing the same genetic clusters. If the priority of the programme is reaching ground cover rapidly the representation of different clusters in the source sample may be adjusted according to a tradeoff between expected gain in growth rate while keeping a broad genetic basis that insures evolutionary resilience.