Quinua (Chenopodium quinoa Willdenow) is a pseudocereal of Amaranthace family which originated from the Andes of South America. Quinoa is an interesting plant whose capacity to tolerate adverse environmental factors and exceptional nutritional qualities warrant further research in all fields of plant biology, agronomy, ecology and biotechnology. Presently, it is an underutilized crop, which has the potential become a major crop. It has increases in importance in the world due to the nutritional quality of its grains and crop adaptability to diverse climatic conditions. In Colombia, more accurately in the Department of Narino, Cauca, Cundinamarca y Boyaca currently Quinua has had a huge boost due to their agronomic potential and different benefits derived from the production, processing and marketing of its products. The objective of this research was to characterize the genetic diversity of a collection of 82 materials of with seven microsatellite markers [inter-simple sequence repeats, (ISSRs)]. The analysis by the coefficient of Nei-Li at the level of similarity of 0.65 divided the population into four groups according to the site of origin of the materials. The value of average heterozygosity was 0.38 which is considered low compared to other studies of genetic diversity in Chenopodium. Molecular Analysis of Variance (AMOVA) and Fst demonstrate the existence of genetic variability at the intraspecific level that should be used in breeding programs of the species lead to obtaining new and better materials of quinua. Key words: Genetic diversity, microsatellites, Andean cereal.