This study was conducted to determine the effects of seed storage method ($-20^{\circ}C$, $2^{\circ}C$ dry, $2^{\circ}C$ wet 30 days, $2^{\circ}C$ wet 60 days, stratification and room temperature) and shading treatment(control, 50%, 80%) on seed germination, seedling growth of endangered species, Iris dichotoma and Iris setosa. As a result, seed germination rate of I. dichotoma was the highest at 75% when seed were stored at $2^{\circ}C$ wet 60 days and then sown under non-shading condition. The seed of I. dichotoma belong to intermediate seed. Seed germination rate of I. setosa was the highest at 95% when seed were stored at $2^{\circ}C$ wet 60 days and then sown under 80% shading condition. The seed of I. setosa belong to recalcitrant seed. Seedlings of I. dichotoma and I. setosa showed not only the best seedling quality but also seedling vigor index in seed stored at $2^{\circ}C$ wet 60 days under non-shading condition, with the growth characteristics of plant height (6.4, 7.2 cm), number of leaves (3, 4), leaf width (4.6, 3.2 mm), leaf length (5.7, 6.8 cm), fresh weight (aerial/root part; 144/260, 97/153 mg), dry weight (aerial/root; 31/20, 17/17 mg) and seedling vigor index and modified seedling vigor index (13,895/9,479, 13,256/8,668). In this research, I. dichotoma and I. setosa seed were stored at $2^{\circ}C$ wet 60 days, and then sown in non-shading condition, seed germination rate was more than 75%, 90%, respectively, and production of superior quality seedlings.