Garlic (Allium sativum .L) has been and is clonally propagated, because it does not produce seed under standard conditions. Knowledge of plant recourses genetic diversity can be a first and most important step in achieving breeding program purposes. Because of its high accuracy and reproducibility among different genetic diversity assessment techniques Amplified Fragment Length Polymorphism (AFLP) has its unique importance. To discriminate among closely related garlic clones AFLP was applied to Analyze the genetic relations among Iranian garlic clones. Thirty-seven clones collected from the main cultivation areas of Iran were analyzed to evaluate their genetic diversity. A total 330 unambiguous bands were obtained by five primer combinations of EcoRI+3 and MseI+3, of which, 231 demonstrated clear polymorphism, representing 69% of total bands. Dendrogram obtained from Unweighted Pair Group Method with Arithmetic Averaging (UPGMA) using the coefficient of Jacard clustered Iranian garlic clones in 8 main groups, then the AFLP results were compared with morphological analysis. Based on AFLP results there existed relative high similarities among groups (0.58- 1) even though some of the clones showed very high similarity (>0.95). Sixteen clones in the 1st and 5th group shared 100% of bands of each group indicating that they are likely duplicate ones. In general there were not any significant relationships detected between genetic diversity and geographical origins. Clones of different ecological climates were classified in one group and in some cases clones that had close origins were clustered with clones from other geographical areas. The potential use of AFLP could show not only the differentiation among species, but also between botanical varieties and well-defined ecotype groups. Finally it can be concluded that AFLP fingerprinting technique with discrimination of duplicate accessions in germplasm collection can decrease costs of conservation of plant material, especially in the case of garlic that is propagated by asexual reproduction. The results of AFLP were in broad agreement with the morphological classification.