Background and aims: In the Atacama Desert certain plant species can be found in small and isolated areas, limited to regions with water availability. The degree of connectivity within and between these natural populations depends on their pollen and seed dispersal abilities, as well as on the barriers imposed by the landscape. Prosopis flexuosa is a species of high economic and ecological importance included in the algarrobo Conservation and Management program. The main objective of this work is to analyze the genetic variability and mating system of P. flexuosa in the Atacama Desert. M&M: Genetic diversity parameters as well as the mating system were evaluated in a natural population (Quillagua) based on microsatellite molecular markers. The hierarchical distribution of genetic variance and kinship coefficients were analyzed. Results: The results indicate high levels of genetic diversity (H-E = 0.67-0.65; Ar = 3.83.7), high outcrossing rates (t(m) = 0.97, t(s) = 0.85), low biparental inbreeding (11.6%) and multiple paternity. The proportion of full sibs decreases when considering seeds from the same or different pods (89 -*16%). Only the variance between families is significant (p < 0.001) and mean kinships estimated show that progenies within families are not only constituted by half sibs. Conclusions: The results are discussed and related to the limited pollen and seed dispersal and their implication for the management of this resource. The study of the mating system parameters of this Chilean desert population suggests that the low population density and the environment fragmentation would not be influencing their mating capacity.