Mooseer or Persian shallot (Allium hirtifolium Boiss.) is a bulbous perennial herb belonging to Alliaceae family. Genetic diversity of 16 mooseer populations collected from different parts of Iran were evaluated using 14 morphological traits as well as antioxidant activities and RAPD markers. Statistical analysis showed significant differences among populations for all morphological traits. In a principal component analysis, four components showed 77.5 % of the total morphological variation. Based on the morphological traits, populations were divided into five groups by clustering. Antioxidant capacities differed among all populations, with the Sahneh and Nahavand populations having the highest and the lowest activities, respectively. Genetic diversity of populations was also investigated through RAPD technique using 14 random primers. Cluster analysis based on RAPD markers plus 47 % coefficient of similarity divided the genotypes into six distinct groups. The highest and lowest similarities between populations were detected to be 0.63 and 0.21, respectively. These results indicated that the assessment of genetic diversity in Iranian mooseer populations could be appropriately carried out using RAPD technique which correlates with morphological traits. Keywords Mooseer Principal componen
