The purpose of this paper was to compare quality of seeds of two black and yellow soybean and the response of plants developed from these seeds to oxidative stress during vegetation and reproduction period. Content of carbohydrates: cellulose, starch, total and reduced sugars, as well as oil and protein content varied among all varieties, irrespective the colour. Bearing in mind all differences in seed quality, as well as response to oxidative stresses during development, black cultivars could be proposed as an excellent source of phenolic compounds (flavan-3-ols, antocyanins, genistein, glycitein, quercetin, laricitrin and isorhamnetin derivatives). Due to extreme fluctuation in precipitation amounts in the last years, information on the better performance of soybean varieties in oxidative stress conditions is of great importance to organic and conventional production of this cultivar.