In this study, using morphological traits and 15 RAPD primers, genetic diversity of 24 satureja genotypes were assessed. There were significant differences among genotypes in all traits. Based on RAPD data, 100 bands were detected and from these 100 bands, 81 bands were polymorph. The mean numbers of bands were 6.7 per primer. According to similarity matrix of molecular and Euclidean distances of morphological data, similarities ranged between 0.61-0.94 (RAPD marker), and 0.38-092 (morphological traits). Based on molecular data the highest similarities belonged to genotypes number F11, F72 (0.94, RAPD marker). Based on morphological traits, the highest similarities belonged to genotypes number A2, B35 and C11, E6 (92%). Cluster analysis showed that the distinctions based on morphological traits did not confirm the distinction based on molecular data. A dendrogram was prepared on the basis of a similarity matrix using the UPGMA algorithm and separated the 24 genotypes into four groups. Our results also indicate that RAPD approach and morphological analysis seemed to be best-suited for fingerprinting and assessing genetic relationships in Satureja genotypes with high accuracy. results showed that RAPD markers could be useful tools for investigating genetic diversity in species of Satureja speciesp.