Background: The object of this work was to determine the genetic and allelic diversity of Solanum species present in Chile, assessing allelic distribution among native varieties and commercial cultivars of Solanum tuberosum ssp. tuberosum L., using microsatellite markers. Results: A high level of allelic richness was found in the potatoes studied. The seven microsatellite markers used presented a total of 64 allelic variants among native varieties and commercial cultivars of Solanum tuberosum ssp. tuberosum. The SSR loci generated an average of 9.16 alleles/locus. The group with the highest PIC was that of native varieties collected in the Chiloe archipelago. The high PIC values found indicate that the native varieties from Chiloe have a low level of interrelation, representing wide genetic diversity. Conclusions: The markers with the highest number of alleles in native varieties corresponded to loci STG 0016 and LEMALX. Commercial cultivars do not present the same genetic variability as native varieties, and the allelic richness of commercial cultivars is lower than that of native varieties of S. tuberosum ssp. tuberosum. Most of the native varieties were clustered in accordance with their geographical location, while commercial cultivars, were clustered in accordance with their breeding programs in Chile and Europe, with the exception of Shepody.