Elaeagnus angustifolia L. is a Eurasian tree that has become naturalized and has various ecological, medicinal and economical uses. In this study, a combination of morphological traits and RAPD markers were used to study the presence or absence of an association between genetic variation and morphological features among five populations of E. angustifolia collected from the East Azarbaijan of Iran. Data analysis of 19 different morphological traits, according to Nei’s genetic distance matrix using Nei’s in GenAlEx 6.5, showed that genetic distance coefficient ranged from 0.014 (between Jolfa and Ahar populations) to 0.86 (between Jolfa/Marand and Meianeh populations). The cluster analysis based on UPGMA and dendrogram plotted using NTSYSpc 2.02 software, revealed 4 main clusters. RAPD analysis using four random primers generated 29 polymorphic bands. Accordingly, the samples were placed in 4 groups. Based on Nei’s genetic distance matrix, a great genetic distance existed between Jolfa and Meianeh populations (0.167) and great genetic similarity existed between Jolfa and Marand populations (0.955). In this research, the results of morphological traits and RAPD markers showed more consistent with each other. Our results showed that RAPD analysis is a suitable method to study genetic diversity and relationships among E. angustifolia populations.