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Chrysanthemum is one of the world's most important cut flower crops. The genetic diversity assessment among present Iranian Chrysanthemum cultivars are needed for future Chrysanthemum breeding programs. In an attempt to reveal the genetic variation and relationship among 30 Chrysanthemum cultivars, some morphological and a chloroplastic gene (rpoC) DNA molecular markers were employed. Chrysanthemum cultivars were cultivated in a Randomized Complete Block design (RCBD) with 3 replications in the field. Meanwhile, a phylogenetic tree was constructed based on chloroplast rpoC gene sequence. Analysis of variance (ANOVA) indicated that a significant variation exists among the Chrysanthemum cultivars for almost all the traits under study. In general, phenotypic coefficient of variation was higher than the genotypic coefficient of variation indicating the predominant role of environment effects. Ward Cluster analysis divided cultivars in two main clusters with highest number of cultivars falling under cluster I. Phylogenetic relationships among Chrysanthemum cultivars based on Maximum likelihood method showed that Iranian cultivars belong to Chrysanthemum morifolium, suggesting that these cultivars have presumably been bred from the same set of parents. Furthermore, genetic distance between cultivars ranged from 0.4 to 2.9, indicating sufficient genetic diversity among cultivars for crossing and selecting the most appropriate parents for Chrysanthemum morifolium breeding programs.