Chrysanthemum morifolium is one of the most important ornamental plant with medicinal effects which has a wide variety of breeding cultivars. The study of diversity (including morphological and molecular) in the next breeding steps including selection, is important. In addition, the study of the phytochemical characteristics of the plants with medicinal properties and the selection of superior cultivars is also an important step in the process of breeding of these plants. One of the strategies to increase the secondary metabolites of the plant is the use of biotic and abiotic elicitors that can affect the metabolic pathways of secondary metabolites and increase their production. This study aimed to evaluate the morpho-phenological, molecular, phytochemical, pollination status and antibacterial activity of different Chrysanthemum cultivars. In addition, the ability to increase the flavonoid compounds and also the expression of the key genes involved in their synthesis pathway under drought stress was investigated. For this purpose, 30 cultivars were planted in a randomized completely block design with three replications at Research Farm of Isfahan University of Technology in 2015. The evaluation of morpho-phenological and agronomic traits during the two consecutive years showed a wide range of variation among different cultivars. The highest percentage of heritability was attributed to fresh weight of flower and days to color appearance of flower bud. Correlation analysis between variables showed that flowering durability was affected by plant morphology. The present research is the first study to investigate the genetic relationships between different Iranian Chrysanthemum cultivars with SRAP markers. The results revealed the potential of SRAP markers to produce polymorphism between Chrysanthemum cultivars. The highest values of the PIC were attributed to Me2-Em3 and Me4-Em3 markers. Comparison of self pollination among different cultivars showed that 22 cultivars out of 30 succeeded in producing self-pollinated seeds. The cultivar Bolor which had the highest self-compability percentage and germination rate as well as the germination percentage of seeds higher than 50% was superior to other cultivars in terms of the production of self-pollinated seeds. Identifying superior and weaker phenotypes as well as genetically identical and distinct cultivars allows for the identification of cross hybridization containing heterosis. According to the results, the evaluated cultivars had a high diversity in terms of all phytochemical traits including total phenole, flavonoid and anthocyanin content as well as antioxidant activity. HPLC analysis showed the presence of eight important compounds including chlorogenic acid, p-coumaric acid, gallic acid, ferulic acid, rutin, luteolin, quercetin and apigenin in the phenolic extract of the studied cultivars. Considering that chlorogenic acid and luteolin are considered as marker compounds for the quality control of Chrysanthemum, Cultivars Bolor, Mehrnoosh2 and Khalij fars2 with high amounts of these compounds can be used as rich antioxidant sources in the food and pharmaceutical industries. Among the studied cultivars, “Shokoh”, “Tarannom2”, and “Sahel” recorded as the highest essential oil contents as well as high flower yields. GC-MS analysis of the essential oil revealed camphor, chrysanthenone, chrysanthenyl acetate, verbenol, (+)-5-epi-neointermedeol, and aromadendrene as the main constituents. In this study, important compounds such as rutin, quercetin, luteolin, apigenin, chlorogenic acid and ferulic acid were identified in the leaves of Iranian Chrysanthemum cultivars. Accumulation of these compounds under drought stress was mainly due to increased expression of the key genes involved in their synthesis route, as well as the interactions of these genes with the environment. The results of the present study suggested the possibility of using drought stress as the abiotic stimulant for increasing the secondary metabolites of Chrysanthemum . Key words Chrysanthemum , Genetic diversity, Essential oil, Anthocyanin, Drought stress, Phenylpropanoid.