Barnyard grasses are dominant weed that are not eliminated easily in the direct water seeding cultivation. So, deep water treatment can reduce their growth at the early growing stage of submerged paddy. This study was carried out to investigate the reducing growth of the barnyard grasses through flooding at seedling stages of rice plant in the green house. Under the normal condition, the plant height of rice variety, Samgwangbyeo, and 3 species of barnyard grass, E. caudata, E. pratocola and E. utilis were not showed the difference up to 10 days after seeding while the plant height of 3 barnyard grass species, especially E. utilis, was more elongated than the rice at 25 days after seeding. Plant height of the 3 barnyard grasses were not elongated largely during 3, 5 and 7 days of flooding treatment at 10 days after seeding. Interestingly, the rice seedlings was grown over 20 cm, and the flooding tolerance of rice seedling was higher than the 3 barnyard grass varieties. However, after flooding treatment for 3, 5 and 7 days, the elongation of plant height of 3 barnyard grasses, especially E. utilis was more speedy compared to rice seedlings as 6 to 9 days passes. And the protein spots from barnyard grasses were also reduced and eliminated more than the spots of rice seedling after flooding treatment.