Sainfoin ( Onobrychis viciifolia Scop.) is widely grown as forage and pasture legume in Iran and is tolerant to environmental stresses. Despite wide geographical occurrence in Iran, little information is available on genetic diversity of sainfoin accessions and their similarity with accessions of other countries. Although molecular markers have been successfully used to determine genetic diversity and characterized cultivars and accessions of some forage legumes but no report is available in sainfoin. To investigate the genetic diversity in Iranian and foreign geromplasm of sainfoin based on morphological characteristics, ISSR marker and botanical characteristics, three experiments were conducted during 2010-2011. In the first study, genetic diversity between 56 accessions (including 46 Iranian and 10 foreign) were evaluated for morphological traits using multivariate statistical analysis. The results indicated considerable variation between studied germplasm for all traits and a better performance for Iranian accessions. The estimation of broad sense heritability for plant height, number of stem per plant, number of stem per meter square and number of nod per stem was high suggesting contribution of the major genes for controlling this traits. Cluster analysis could separate Iranian and foreign sainfoin accession on the base of morphological traits. Moreover accessions of similar geographic origin were mainly clustered in same groups. Stepwise regression for dry matter yield and forage palatability showed that number of stem per plant and plant height explained the majority of the variation. In the second study, genetic diversity between 75 accession (43 Iranian and 34 foreign) were evaluated using ISSR technique. From 22 primers, 239 polymorphic markers were scored to differentiate between accessions. Accordingly ISSR analysis revealed that Iranian accessions were more diverse than foreign accessions. Applying complete linkage method of cluster analysis Iranian and foreign sainfoin accession were clustered in different groups and each clustered into four groups that largely supported the known origins and some morphological characteristics of these accessions. Also The PCOA was confirmed the result of cluster analysis. The analysis of molecular variance (AMOVA) based on specified geographic regions, showed that majority of the genetic variance was found among the accessions and less among the geographical groups. Although a moderate correlation (r=0.5 * ) was found between morphological and ISSR data, ISSR data could better differentiate the sainfoin accessions indicating that this technique is an efficient tool for justify; MARGIN: 0in 0in 10pt" Key words: Anatomy, genetic similarity, sainfoin, molecular marker, morphology, Phylogeny