Sardari is one of the most important landraces of common wheat (Triticum aestivum L.) that is mainly cultivated in drylands and mountainous area of Iran. Moreover, it shows a high level of genetic diversity. In the present research a total of 73 Sardari wheat ecotypes were evaluated for drought tolerance. Genetic diversity was analyzed using amplified fragment length polymorphism (AFLP) MARKER based on three pairs of primer combinations. Of the 2,431 AFLP bands detected, 1,582 (73.92%) were polymorphic. Cluster analysis divided all ecotypes into eight major groups. Ecotypes also showed genetic diversity for drought tolerance and were classified into three groups. The first group consisted of forty-two of the 73 landraces and had a low stress tolerance index (STI), ranging from 0.165 to 0.401, while the second (23 landraces) and the third group (7 landraces) had a medium and high STI ranging from 0.425 to 0.640 and 0.662 to 0.817, respectively. Discriminant analysis (DA) identified twenty-four MARKERs selected from 218 AFLP MARKERs that accounted for the difference between the three phenotypic groups. By using the selected MARKERs, DA validated the phenotypic grouping, with a zero error rate. The results showed a high degree of genetic diversity between the Sardari ecotypes, suggesting that Sardari can be used as a germplasm source for wheat improvement toward releasing more desirable cultivars.