Quinoa cultivation in Chile presents an ancient and active complex of geographic, climatic, social and cultural interactions that has determined its current biodiversity in the three main growing zones (north, centre and south). These interactions consider a central issue viz. the participation of farmers, whose activities are at the base of seed exchanges networks due to their knowledge and in situ conservation of genetic diversity. In this study we report antecedents that contribute to a better understanding of seed exchanges through the analysis of field works assessing the key roles of farmers involved in the biodiversity dynamics and characterization of 20 microsatellites genetic markers in a multi-origin set of 34 representative quinoa accessions of Chile and South American region. The phenetic analysis of germplasm (UPGMA) was consistent with the current classification of quinoa ecotypes present in Chile and Andean zone. This allowed the identification of five population, which were represented by quinoa of Salares (northern Chile), Coastal/Lowlands (central and southern Chile), Highlands (Peru, Bolivia and Argentina) and Inter-Andean Valleys (Ecuador and Colombia). The good informative quality of the markers used revealed a wide genetic diversity among main growing areas in Chile, which correlates well with natural geographical-edaphic-climatic and social-linguistic context to the expansion of quinoa biodiversity. Additionally, the ancient seed exchanges reveals this process is still governed by an array of diverse agricultural practices of Andean farmers. Genetic erosion is considered a imminent risk due to small scale farming, where the increased migration of people to urban systems and exportation-driven influence can further reduce the cultivated diversity.