Understanding milk thistle genetic diversity is essential for breeding programs of this plant. In order to investigate genetic diversity of some Iranian ecotypes, an experiment was performed based on randomized complete block design in three replications using Iranian collected ecotypes and foreign cultivar "Bodaklazi" in the experimental field of Shahid Chamran University . Morphological traits including plant height, diameter of the main capitol per plant, number of capitol in plant, grain number in capitol, grain weight in capitol, thousand kernel weight, grain yield, starting and ending days to flowering, and phytochemical traits including phenol level, flavonoid level and antioxidant capacity were measured. Analysis of variance showed significant differencs (α ≤ 0.01) for different traits. Sari and Mobarakeh showed the highest performance among ecotypes. The phenolic and flavonoid content and antioxidant capacity of ecotypes ranged between 8.18-14.19 mg Tanic acid per g plant matter,5.36-11.08mg per 100g and 32.07-52.40 mg per 100g dry extract respectively. Silymarin ranged between 32.07 and 55.40 mg per 100g dry extract. Cluster analysis indicated that ecotypes can be divided into two major groups. Thus, Molasanie, Amol, Sari, Ahvaz, Shoushtar, Esfahan, Babol and Njafabad were categorized in one group and Mobarakeh and Majari in one another. The results of this study showed that the Iranian ecotypes of milk thistle inherit noticeable diversity in respect to morphological, phonological and phytochemical traits. This diversity can be used in breeding programs.