Nine natural populations of Moroccan Medicago truncatula were analysed using enzymatic markers to identify useful phytogenetic resources for their integration in programmes of safeguard and conservation. Starch gel electrophoresis was used to examine genetic variation within and among natural populations. According to our estimates of genetic variation analysed by five loci detected for three enzyme system, the species showed a high genetic diversity. 46% of the total variation is due to the diversity between populations. It appears that a considerable variation was found among populations, indicating an interesting genetic potential for selection. This result is in accordance with the strictly autogamous system of reproduction in this species. The dendrogram generated from pairwise genetic distance among all populations showed three distinct clusters independently from the geographic origin. Conservation programs should take into account the level of genetic diversity within and between populations revealed by isozyme markers.