Milk thistle (Silybum marianum L .) is a plant belonging to the family Asteraceae and is known as an effective herbal medicine in treating liver diseases. This study was conducted to study the effects of breeding system and self and cross-pollination on silymarin and some agronomic traits of 11 ecotypes of Milk thistle under normal and drought stress conditions in three studies in growing season of 2013 in the research field of Isfahan University of Technology. The first study was conducted to investigate genetic diversity and reproductive characteristics of ecotypes according to a randomized complete block design. Results showed that ecotypes had a high genetic variation for most of the traits. percentage of dead pollen grains had a negative correlation with number of seeds in the capitol. In the trait of pigmentation, it was found that ecotypes of northern areas had darker color. Also the traits seed weight per capitol decreased by increasing the length and diameter of flower seeds. Second study was done to evaluate effects of pollination system and moisture environment on Milk thistle ecotypes and it was performed in the field according to a combined analysis of split plot design. To estimate obligate selfing effects, at flowering time some capitols of each plant enveloped before flowering and the others were allowed for cross pollination. Results indicated that effect of moisture envionments and pollination system were significant on the most of measured traits. Significant differences was observed among the ecotypes for seed color, seed width, seed diameter and percentage silymarin content. Self pollination reduced percentage of oil and silymarin content and increased grain size and grain weight. Negative correlation between seed color and oil content were observed. Third study was performed to evaluate the effect of maternal environment (normal and drought stress in field) on seedling traits and drought tolerance in seedling stage under two levels of osmoticotential(0, -8 bar) byolyethylene glycol (PEG). In general, seeds from maternal environment stress in comparison to normal condition, had less germination percentage, root length and root dry weight. Self-pollinated seeds had higher values of root length than seeds resulted from cross-pollination but the values of shoot length were reduced by self-pollination. However self and cross-pollination treatments had no significant effects o seed germination. Drought stress caused by PEG decreased the studied traits significantly compared to control condition indicating low drought tolerance of this species during germination stage. Finally results indicated that considering no inbreeding depression by self-pollination in this plant, production of pure inbred lines is possible in order to plan future studies in this medicinal plant. Keywords : silymarin, pollination, seedling, milk thistle, morphological characteristics