Accurate and reliable cultivar identification of crop species is essential to ensure plant material identity for registration and for cultivar protection. In this article, we proposed six simple sequence repeat (SSR) loci as a sufficient tool to characterize fig (Ficus carica L.) germplasm in Morocco maintained in an ex situ collection. A set of 17 microsatellite loci was used to characterize 75 accessions representing eight caprifigs, 51 local accessions, 11 foreign accessions, and five accessions of unknown origin. Eighty-five alleles with a mean number of six alleles per locus were observed in 62 distinct genotypes. Suspected synonyms and homonyms were confirmed, some of which maybe resulted from somatic mutation. Based on genetic criteria, including linkage disequilibrium, discrimination power, and molecular criteria as polymerase chain reaction conditions of loci multiplexing, we proposed a key identification set using six microsatellite markers to discriminate all genotypes present in the ex situ collection. Our selected SSR loci set can be used for larger genetic studies of fig germplasm, and a similar approach can be adopted for other fruit species