This study characterized the genetic diversity of 18 Tunisian fig cultivars using random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR). Both random and ISSR primers tested generated a total of 116 RAPD and 47 ISSR markers. Considerable genetic variation was observed among fig cultivars sampled from two regional Tunisian collections with an average diversity of 4.57. RAPD and ISSR banding patterns and genetic distances values reflected the high level of diversity among the collections and lower variability between the two collections. The correlation between the RAPD and ISSR similarity matrices computed for the 153 pairwise comparisons among the 18 varieties was lower and significant. An analysis of molecular variance showed that 92% of the total genetic diversity resided within collections, whereas only 8% between collections. The results indicated that in the local fig germ plasm the information provided by RAPD and ISSR is not analogous, most likely as a consequence of the fact that the two classes of markers explore, at least in part, different portions of the genome.