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The intraspecific evolutionary history of South American xerophytic plant species has been poorly explored. The tree species Prosopis chilensis has a disjunct distribution in four South American regions: southern Peru, southern Bolivia, central–western Argentina and central Chile. Here, we combined phylogeographical (based on chloroplast and nuclear markers), morphological and climatic data to evaluate the relative contribution of historical demo-stochastic and adaptive processes in differentiating the disjunct areas of distribution. The results obtained with the two molecular markers revealed two closely related phylogroups (Northern and Southern, predominating in Bolivian Chaco and in Argentine Chaco/Monte, respectively), which would have diverged at ~5 Mya, probably associated with transgression of the Paranaense Sea. Bolivia and Argentina have a larger number of exclusive haplotypes/alleles and higher molecular diversity than Chile, suggesting a long-lasting in situ persistence in the former and a relatively recent colonization in the latter, from the Bolivian and Argentinian lineages. The two main lineages differ in morphology and climatic niche, revealing two significant, independent evolutionary units within P. chilensis promoted by local adaptation and geographical isolation. [ABSTRACT FROM AUTHOR]