Retrotransposon movements are considered to be an important factor in evolutionary processes and speciation as well as a source of genetic variation. In order to analyze genetic diversity and population structure in Tunisian pistachio species, nine inter-retrotransposon amplified polymorphism (IRAP) markers were used. As a result, eighty-six amplicons were produced among which 98.15 % were polymorphic. Mean numbers of the effective number of alleles (Ne), Shannon’s information index (I) and Nei’s genetic diversity (H) were respectively 1.529, 0.478, and 0.310. The average within-population genetic diversity (Hs) was 0.24 and the total diversity (Ht) was 0.3. The Tunisian pistachio populations exhibited high genetic differentiation (Gst =0.275) and gene flow (