The objectives of this study were to select the seeds of Cucurbitaceae and Solanaceae genotypes in terms of superior with bioactive compounds content and to inform sophisticated data for developing the high value-added products. We evaluated to aspects of the antioxidant activity, polyphenol content, and flavonoid contents in seeds from two vegetable family. We used in the Cucurbitaceae(watermelon, squash, bitter gourd, and sponge gourd) and Solanaceae(hot pepper, sweet pepper, and egg plant) the total 408 genotypes. In Cucurbitaceae, polyphenol content of watermelon and squash genotypes were ranged 19.9-343.8 and 6.1-81.2 mg·100 g-1 DW, respectively. The polyphenol content of watermelon genotypes was 12% among all genotypes over 160 mg·100 g-1 DW. The mean of flavonoid content in watermelon and squash genotypes represented 80 and 41.3 mg·100 g-1 DW, respectively. In Solanaceae, flavonoid content of hot pepper genotypes was ranged 64.4-472.5 mg·100 g-1 DW, with an average of 165.0 mg·100 g-1. The 23 hot pepper genotypes were classified over 90% antioxidant activity. The antioxidant activity of sweet pepper was ranged 35.9-90.3%, and 23% of all genotypes represented 82% antioxidant activity. The polyphenol and flavonoid content of egg plant was ranged 38.1-642.0 mg·100 g-1 DW and 14.2-1217.0 mg·100 g-1 DW, respectively. In addition, we selected that 8 egg plant with the superior genotypes for antioxidant activity, polyphenol, and flavonoid content. Results revealed that there was significant variation of antioxidant activity and bioactive compounds contents in both vegetable famaily. In addition, we suggested that selected genotypes seeds with high contain bioactive compounds will be more efficiency to develop natural value-added products.