Allium L. (Amaryllidaceae), as one of the largest genera of monocots, comprises more than 900 species naturally occurring on the Northern Hemisphere. There are about 100 species of Allium in Iran of which a large number have a great potential to be introduced as ornamental plant.In this study the genetic relationships and genetic diversity of 11 Allium species from Khorassan province of Iran including 32 accessions were investigated by inter simple sequence repeat (ISSR). Nine ISSR primers produced a total of 80 polymorphic markers and revealed high polymorphism among the studied species. The average gene diversity, effective number of alleles and Shannon’s information index were 0.2, 1.28 and 0.3, respectively. A. kuhsorkhense exhibited the greatest level of variation (He: 0.17), whereas A. stipitatum demonstrated the lowest level of variability (He: 0.05). The unweighted pair group method arithmetic average (UPGMA) analysis showed that accessions have a similarity range of 0.60 to 0.95. A. scapriscapum composed the most distant group in the dendrogram. The dendrogram clustered Allium accessions in high correspondence to infrageneric classification of the genus. The present study showed that the ISSR technique is an effective molecular approach for analyzing genetic diversity and genetic relationship in Allium species.

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