Carrasco, B.;Garces, M.;Rojas, P.;Saud, G.; Herrera, R.; ; Caligari, P.D.S. Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, Talca, Chile. Retamales, J.B.Facultad de Ciencias Agrarias, Universidad de Talca and Centro de Investigación en Biotecnología Silvoagrícola (CIBS), Universidad de Talca, Talca, Chile.The chilean strawberry displays high fruit quality and tolerance to abiotic and biotic factors. Additionally, this species has a rich cultural history going back for at least several thousand years in association with aboriginal people activities and continues at a reduced level today. After its introduction to Europe during the 18th century, it formed an interspecific hybrid to become the maternal species of the commercial strawberry, Fragaria xananassa Duch. The objectives of the current investigation were to determine the level and patterns of partitioning of intersimple sequence repeat (ISSR) diversity. ISSR markers were used to assess the genetic diversity in 216 accessions of F. chiloensis, which represented the two botanical forms present in Chile [F. chiloensis ssp. chiloensis f. chiloensis and F. chiloensis ssp. chiloensis f. patagonica (L.) Duch.]. Our results showed high genetic diversity at the species level [polymorphic ISSR loci (P) = 89.6%, gene diversity (h) = 0.24 ± 0.17, Shannon's index (S) = 0.37 ± 0.24] and a lower genetic diversity in f. chiloensis than f. patagonica. The analysis of molecular variance (AMOVA) showed a moderate genetic differentiation among accessions (st = 14.9%). No geographic patterns for ISSR diversity were observed. AMOVA, structure, and discriminant analysis indicated that accessions tend to group by botanical form. The impact of domestication on the genetic structure of chilean strawberry and its application to breeding and conservation are discussed.