A collection of 130 olive samples, originating from diverse areas in Europe and corresponding to 67 different cultivars denominations, was genotyped at 14 microsatellite loci. In total, 135 alleles with a mean number of 9.6 alleles per locus were detected. All but 30 accessions showed unique genotypes. Several cases of synonymy listed in the FAO database of olive germplasm could not be confirmed, as different allelic profiles were obtained from putatively synonymous cultivars. The existence of homonyms or mislabeled samples in olive germplasm collections was evidenced by allele differences of up to 60% between samples of the same denomination. An allele-sharing phenogram of the analyzed genotypes revealed several cultivars with high levels of intra-varietal polymorphism, as well as cultivar families consisting of closely related cultivars with similar denominations. Our work shows that the current designations of olive cultivars fall short of describing the genetic variability among economically important plant material. A thorough investigation of the existing variability will prove of major importance for both management and economic production of olive trees.