Onion ( Allium cepa L.) is the most important edible Allium species, recorded for over 4,000 years and ranks second in value among cultivated vegetables. Onion is an outcrossing, biennial, diploid (2n=2 x =16) plant with a very large (32 pg/2 n) genome. It is proposed that the southwest Asian gene center of A.cepa should be acknowledged as the primary center of domestication and variability, whereas other regions such as the Mediterranean basin, where onion has a great variability, are secondary centers. it is believed that with many landraces of onion exist across the Iran and a longstanding history of cultivation, Iran is rich in genetic diversity of onion. Despite many morphological study, little is known regarding the genetic relationships among germplasm of onion in this country. Therefore, the objectives of this study were based on determining genetic variations among onion landraces using Simple Sequence Repeat (SSR) and Inter Simple Sequence Repeat (ISSR) markers. Eighteen Iranian onion landraces collected from different parts of Iran with five foreign cultivars were used. Five plants per landraces were randomly selected, and young green healthy leaves from each plant were collected for DNA extraction. Total genomic DNA was extracted by the cetyl trimethyl ammonium bromaid (CTAB) method with modifications. DNA concentration and quality was determined by electrophoresis in a 0.7% (w/v) agarose gel. Fifteen primer pairs detecting SSR loci in onion were used in the amplification. The number of bands per primer varied from 2 to 6, with mean of 3.3 polymorphic bands and mean heterozygosity of 0.75. A dendrogram based on similarity coffecient and UPGMA algorithm grouped the onion landraces and foreign cultivars into five groups and one independent genotyp. From SSR analysis, a higher level of genetic variation was observed within populations, compared to variation among populations in the onion landraces and foreign cultivars. Highest and lowest mean genetic diversity were obtained in Sephide Gorgan and Yellow Sweet Spanich respectively. Fourteen primers were used for PCR amplification. Amplified DNA fragment were separated elecrtophoretically in a 1/5 (w/v) agarose gel. From these data, a Squared –Euclidian distance matrix was calculated to estimate pair-wise differences in the amplification product for all genotypes. Cluster analysis was done using a UPGMA algorithm to construct a dendrogram. A high degree of polymorphism was observed in the present material. All 14 primers generated 7 to 14 polymorphic bands, and the frequency of polymorphi
