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Mediterranean Hedysarea species constitute important phytogenetic resources able to promote forage production and to valorize grasslands currently damaged by severe genetic erosion. The study of genetic diversity in nine Mediterranean Hedysarea species found in North Africa was performed using the AFLP technique. The eight primer combinations generated, on the whole, 325 polymorphic bands exhibiting an important genetic diversity that constitutes an ideal source stock for germplasm selection. The estimation by AFLP analysis of the relative relationships among six Sulla and three Hedysarum species revealed the genetic nearness of the two analyzed genera as shown by the close relatedness of S. carnosa and Hedysarum species. Our investigation suggested a nuclear lineage among the Mediterranean Hedysarea species. Moreover, a common genetic pool among the analyzed species indicated a common ancestor H. membranaceum generating all the analyzed species. The obtained UPGMA dendrogram exhibited species clustering independently from their bioclimatic origin. This result was confirmed by Pearson’s correlation coefficient (0.097, p = 0.302). Principal component analysis of the obtained AFLP data has also shown mixed species. In fact, the distribution in plan 1-2 (34.34% of the global inertia) showed typical continuous variability since there is no distinctiveness of species. The close congruence of the only cultivated Sulla species (i.e., S. coronaria) and the spontaneous S. flexuosa, which is affected by severe genetic erosion, could permit including these species in amelioration programs for improvement of forage crops. Moreover, the related proximity of the semi-temperate species S. capitata and H. aculeolatum, respectively, to the arid/semi-arid species S. carnosa and S. spinosissima could be exploited in breeding programs to improve the damaged southern Tunisian grasslands, especially in arid and semi-arid areas.