We evaluated the genetic diversity of Iranian Mooseer (Allium stipitatum Regel. syn. A. hirtifolium Boiss.) using morphological traits and AFLP markers and determined the phylogenetic relationships and the position of Iranian Mooseer among domesticated and wild edible alliums using internal transcribed spacer (ITS) sequence data. Four EcoRI and MseI AFLP primer combinations rendered produced 376 markers, 204 being polymorphic (53.28% polymorphism). AFLP data separated clearly the Kazeroun accession, originating from the warmer Southern region of Iran, from the other 20 accessions. According to the morphological evaluation data, Khansar, Kouhrang and Daran accessions showed the highest means for bulb weight. Cluster analysis based on morphological traits divided the Mooseer germplasms into three main groups. The ITS results indicated that Iranian Mooseer clustered with other A. stipitatum accessions, but with small differences. They were phylogenetically close to Iranian wild edible alliums and clearly differentiated from other domesticated alliums. Separation of three Iranian Mooseers from A. stipitatum samples originated from other countries in two distinct groups according to their ITS sequence shows that probably these two groups have divergent evolutionary paths.