To study the genetic variation of agronomic and morphological traits in 32 genotypes of safflower an experiment was conducted in a randomized complete block design with three replications at Research Farm of Isfahan University of Technology , located in Lavark, Najaf-Abad. Also, genetic diversity of 20 of those genotypes was assessed by RAPD marker. Agronomic and morphological traits of days to 50% germination, days to flowering, days to 50% flowering, days to maturity, plant height, branches per plant, capitula per plant, seeds per capitulum, 1000-seed weight, reaction to powdery mildew, seed yield and seed yield per plant were measured . Analysis of variance showed that genotypes significantly differed for all studied traits. Seed yield and seed yield per plant among the genotypes varied from 1088 to 2168 kg/ha and from 7.15 to 16.43 g/plant, respectively. The highest and lowest genetic variation was observed for seeds per capitulum and days to maturity, respectively. Genetic and phenotypic correlation coefficients showed that number of seed per capitula and number of capitula per plant had the high positive correlation with both seed yield and seed yield per plant. Regression analysis also showed that number of capitula per plant explained 43/6 % and along with seeds per capitula and plant height 60 % of total variations for seed yield. The results of regression analysis for seed yield per plant revealed that seeds per capitula, capitula per plant and 1000-seed weight explained 81.2% of its variation. According to the results of path analysis, capitula per plant had the most direct positive effect on seed yield and seed yield per plant, however, its effect was declined with indirect and negative effect of seed weight. Principle component analysis revealed 6 factors, contributing in 90 of total variations of the traits. Factor analysis also recognized 3 factors which explained 81.81 % of total variations. These factors were named as yield components and plant height, phonological traits and branch factor. Cluster analysis and analysis of variance base on the agronomic and morphological traits grouped the genotypes in to 3 clusters. The RAPD markers revealed 15 polymorphic primers out of 50 tested primers and percentage of polymorphism varied from 37 to 100 percents. Similarity matrix revealed the highest similarity between Ac-Sunset and Ac-Sterling genotypes and the lowest similarity between E 2428 and GE 62923 genotypes. C cluster analysis based on RAPD marker, the genotypes clustered in to 5 groups, using 54% coefficient of similarity. Comparing the results of clustering based of morphological markers with those of molecular markers showed that there were some differences. Thees differences may be caused by environmental effects as well as amplification of non-coding regions in molecular markers. The existing of high variation for morphological traits and polymo