This work aimed to evaluate the chemical composition and the initial growth of soybean seedlings originated from seeds produced under influence of soil flooding in the crop reproductive period. The experimental design was totally randomized, organized in factorial scheme being two soybean cultivars x three soil-flooding periods, and the traits were disposed in four repetitions. When submitting soybean plants to flooding at R5 stage, the mass of thousand seeds was reduced independently of the cultivar. The shoot growth and length, shoot dry matter, and roots dry matter characters were negatively influenced due to soil flooding in R5 growth stage. The oxygen deficiency can cause alteration in roots and shoot protein concentration on soybeans seedlings. The aminoacids concentration was stimulated in roots and shoot of seedlings originated from seeds produced under hypoxia conditions.