Introduction. Ficus carica L., well adapted to the Mediterranean climate, is ubiquitous in Tunisia. In spite of the large possibilities of its adaptation to the Tunisian climate, its cultivation remains traditional. In Tunisia, this species is represented by a large number of varieties which are facing genetic erosion. To save these genetic resources, we studied some of the Tunisian varieties using molecular markers. The aim of this analysis was to study the genetic diversity of some cultivars and to characterize them. Materials and methods. Six microsatellites were used to characterize 16 cultivars (Ficus carica L.) belonging to two fig tree collections in the south of Tunisia. Results. The molecular markers used appeared highly polymorphic in common fig trees since 4–12 alleles per locus and a mean of heterozygoty of 0.656 were scored. The resolving power (Rp) of the six microsatellites tested ranged from 2.12 to 3.87 for the 16 cultivars studied, showing a significant genetic diversity (Ht = 0.762). Genetic differentiation between geographical groups was low (Gst = 0.032). The factorial correspondence analysis showed no well-defined relation between the 16 cultivars and their geographical origin. The genotype patterns allowed us to discriminate all of the cultivars. Conclusion. The characterization of the accessions belonging to different varieties was possible, showing the power and efficiency of the molecular tools used.