Prosopis (Mimosoideae, Leguminosae) genus constitutes an important genetic resource for arid and semiarid environments. In Chile, Prosopis chilensis (Mol) Stuntz, (algarrobo) is the species with the widest distribution range, displaying a high phenotypic variability. Moreover, in Chile the species conforms a periferical metapopulation biogeographically isolated caused by the Andes. The aim of this study was to analyze its genetic diversity in Coquimbo’s Región using six nuclear and eight chloroplastic microsatellite markers. A dendrogram of genetic diversity with nuclear loci displayed 143 genotypes. For chloroplastic analysis, one locus showed five haplotypes. Results suggest no difference between Elqui and Limari and slight but not significant difference with Choapa. This should be corroborated with further studies to the south of its distribution range