Common fig (Ficus carica L.) is an underused fruit crop cultivated in Mediterranean countries since antiquity. In this study, 20 simple sequence repeat (SSR) loci were used to characterize 209 fig accessions conserved in an ex-situ field germplasm collection. A total of 78 fragments were amplified with the 20 pairs of SSR primers, with an average of 3.9 alleles per locus and a size between 120 and 376 bp. The mean expected and observed heterozygosities were 0.36 and 0.41, respectively. The total value for the probability of identity was 6.8 × 10−4. The SSRs studied resulted in identification of 98 unique genotypes (46.86% of all accessions preserved in the bank), indicating a high number of synonyms. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis did not show clear groups based on geographic distance, although some specific groups related to fruit type were observed. The results confirm the usefulness of microsatellites for the identification of genetic diversity and potential value of germplasm management for fig.