Chile is considered to be a sub-center of origin for the cultivated potato, with native and introduced genetic material coexisting in the country. Thus, the different varieties present in Chiloe Island are characterized by a rich diversity of forms, sizes, colours and phenological characteristics. In the present work, the level of polymorphism and the genetic relationship were studied by means of molecular markers using the amplified fragment length polymorphism (AFLP) technique and twenty-seven morphological characters. Twenty varieties of potatoes from the Chiloe Island were analyzed. The commercial variety Desiree and one specie from the Etuberosa series, Solanum fernandezianum, collected in the Juan Fernandez Island were included as controls. A similarity tree-diagram was made, based on all the AFLP bands generated in the range between 65 and 290 base pairs. With these tools, it was possible to identify molecular differences morphological traits such as the predominant forms of the tuber, flower colour and resistance to disease.