Medicago ciliaris (L.) Krock and Medicago intertexta (L.) Mill are most often found in saline regions and are considered aspotential resources for genes related to salinity resistance. To explore the genetic diversity of these two species by mean of nrSSR (simplesequence repeats) markers, 11 accessions originated from different regions in north of Africa and Middle East were chosen. Ten among14 markers turned out to be polymorphic and gave 72 alleles. Eight markers were very informative with PIC values > 0.5, and three ofthem were found to be nonneutral. Allelic richness was limited with an average number of alleles per locus of 2.7. All populations havea significant heterozygous deficit evidenced by both observed heterozygosity rates (null for most populations) and multilocus fixationindex estimates. A strong differentiation between populations was highlighted by FST (0.805) and GST (0.919) values. Low values ofgene flow (0.01–0.38) revealed a very weak gene exchange between populations regardless of the proximity of their sites of origin. Thetotal variability breakdown by analysis of molecular variance (AMOVA test) showed a preponderance of interpopulation component(73%–72%) with respect to intrapopulation one (18%), mainly due to the mating system. Relationship analysis performed by NJ treerepresentation trends to place M. ciliaris as an ancestor and M. intertexta as a derivative. The two populations from the Sebkha site,characterized by the highest variability and more private alleles, constitute an ideal reservoir of genes for tolerance to salinity. Significantgenetic diversity in the two aforementioned species is encouraging for their conservation.