Olives were introduced in Argentina from Europe over 400 years ago. Several cultivars are grown in Mendoza province and problems exist on misclassification of plants in orchards and nurseries. This work was aimed to develop a cost effective protocol for fingerprinting olive germplasm using microsatellites (SSRs) and generate a database in order to help in the identification of olives trees in Mendoza. Four highly informative polymorphic SSRs (DCA3, DCA9, DCA11 and DCA16) were selected to fingerprint olive cultivars. A protocol using a single dye-labeled forward common primer with the M13 (-21) sequence was used in combination with the reverse specific SSR primers. PCR amplifications were multiplexed and resolved in automated capillary genetic analyzer equipment. Profiles of the cultivars and a list of alleles with the sizes obtained by capillary electrophoresis are provided. Several genetic parameters were calculated to characterize the microsatellite loci. A database of SSR markers for eleven of the more distributed olive cultivars in Mendoza was developed.