Iran, is a country with different climates and rich in medicinal plants gene pool. Drought is one of the most important abiotic stresses in this country. Milk thistle ( Silybum marianum ) is one of the valuable medicinal plant because it is well adapted to Iran. The most important medicinal application of silymarinis its use as a hepatoprotectant of liver disease. This plant is native to mediterranean regions and also distributed in some parts of Iran (North, South and West). In this regard, 26 different milk thistle ecotypes from nine provinces of country and two foreign accessions were evaluated in two moisture conditions (non-stress and drought stress). Results showed that there was high variability among the studied ecotypes for all traits except oil content. Results indicated that drought stress significantly reduced the diameter of main capitol and capitol per plant. The comparisons among ecotypes determined ecotype 18 from Khuzestan province showed the highest average silymarin content under both stress and non-stress conditions and ecotype 31(foreign source) produced high yield and silymarin content in stress condition. The highest correlation was observed between yield and the number of capitol per plant in both moisture conditions. Although the correlation between silymarin content with yield in non-stress condition was not significant, there was significant positive correlation between them in stress condition. The biplot of principle component analysis (PCA) in non-stress condition showed that ecotype 16 and 18 from Khuzestan province were appropriate for seed and silymarin production. Results of PCA in stress condition indicated that ecotype 22 (Khuzestan province) and 12 (Elam province) were desirable in silymarin content. The results indicated that drought stress causes reduction in genetic diversity under drought stress. The result of cluster analysis, based on measured traits in both moisture levels could mainly separate ecotypes based on geographical origins. Ecotype 31 (foreign source) was grouped in a separate cluster in both non-stress and stress conditions indicating it has the least genetic similarity with other ecotypes. In conclusion, ecotypes 14 (Khuzestan province) showed the most yield, oil content and silymarin content, ecotype 31 (foreign source) was high in yield and silymarin content in non-stress condition and ecotype 22 (Khuzestan province) showed the most yield and silymarin content in stress condition, which can be used for future breeding programs. Keywords : Milk thistile, genetic diversity, drought stress, oil content, silymarin content