Chile has two certified origin olive products: Extra-Virgin Olive Oil (EVOO) from Huasco valley and the Azapa variety table olive from the Azapa valley. However, efficient methodologies are needed to determine the varieties and raw materials involved in the end products. In this study, we assessed the size of alleles from ten microsatellites in 20 EVOOs and in leaves and fruits of 16 olive varieties cultivated in Chile to authenticate their origins. The identification of varieties relied on specific allele sizes derived from microsatellites markers UDO99-011 and DCA18-M found in leaves and fruit mesocarp. While most Chilean single-variety EVOOs matched the variety declared on the label, inconsistencies were observed in single-variety EVOOs containing multiple varieties. Our findings confirm that microsatellites serve as a valuable as diagnostic tools for ensuring the quality control of Geographical Indication certification for Azapa olives and EVOO with Designation of Origin from Huasco. C1 [Contreras-Diaz, Roberto] Univ Atacama, Ctr Reg Invest & Desarrollo Sustentable Atacama CR, Copiapo, Chile. [van den Brink, Liesbeth] Univ Tubingen, Inst Evolut & Ecol, Plant Ecol Grp, Tubingen, Germany. [van den Brink, Liesbeth] Univ Concepcion, Dept Bot, ECOBIOSIS, Concepcion, Chile. [Tapia, Francisco] Inst Invest Agr, Ctr Reg Invest Intihuasi, La Serena, Chile. C3 Universidad de Atacama; Eberhard Karls University of Tubingen; Universidad de Concepcion