The effect of water deficits on soybean [Glycine max (L.) Merr.] could appear on seed quality through changes of morphological plant characteristics. Two Korean genotypes, Hwangkeum (determinate growth habit) and Muhan (indeterminate growth habit), were used to examine the influences of treatment stage and method of water deficit during reproductive growth period on yield and seed quality of soybean. Water deficit at R5 or R6 stages was as damaging to seed quality as double water-deficit treatments at R2+R5 or R2+R6. However, seed from double water-deficit treatment tended to have lower oxidation-reduction potential compare to the corresponding single water-deficit treatment. In comparison with Muhan, Hwangkeum had significantly greater oxidation-reduction potential value. Seed yield per plant in both genotypes depended greatly on seed yield of branches. However, the proportion of number of branch seed to total seed umber in Hwangkeum was increased as the water deficit was applied during later reproductive stage, whereas, in Muhan the proportion was lower. Water-deficit treatments including the single and double water-deficit treatments and non-stressed treatment were able to be classified into five groups for Hwangkeum and four groups for Muhan based on the influences on yield components, number of pod, number of seed, and single seed weight, using principal component analysis. In both genotypes, R2+R5 water-deficit treatment decreased number of pod and seed, but increased single seed weight. On the contrary, R6 or R2+R6 stress increased the pod and seed number, but decreased single seed weight.