ABSTRACT The south of Colombia is a center of diversity for diploid potatoes in the Solanum tuberosum group Phureja. This germplasm is important for genetic studies and is used as a genetic resource in potato breeding programs. In Andean countries, Phureja group potatoes are a staple food and represent important incomes for smallholder farmers. We studied the genetic diversity and population structure of 110 diploid potato group Phureja accessions by analyzing allele frequencies using a set of 42 microsatellites (simple sequence repeats). The accessions used in this study were 97 diploid S. tuberosum Phureja group accessions from the Colombian Core Collection and 13 diploid accessions from the German germplasm bank. Allelic richness, heterozygosity, population differentiation ( F statistics) and population allocation by means of Bayesian modeling analyses were performed. Results indicated that the population is highly diverse (Hs = 0.55), and genetic differentiation (F ST = 0.09636) is mainly due to differences between accessions (F IS = 0.17115). These indexes of population differentiation suggest a moderate division within the population but not a marked population structure. Results with respect to the genetic structure of the analyzed germplasm provide the basis for the development and implementation of linkage and association mapping as well as methods for precision breeding such as the search for diagnostic molecular markers.