High physiological quality soybean seeds are essential for a successful production, because they promote optimal plant density in the field. The objective of this work was to evaluate the effect of boron doses applied at different phenological stages of two soybean varieties on the physiological quality of the seeds. Two field experiments were carried out, one with each variety of soybean, conventional and transgenic. Five doses for boron were applied to the soil as boric acid (17%): 0, 1.0, 2.0, 3.0 and 4.0 kg ha-1, at three phenological stages (V6, V9 e R1). In R8 stage the seeds are harvested and then tested for physiological quality, through the tests of Germination, germination first count, germination speed index, accelerated aging and electrical conductivity. For the conventional variety, the boron doses promoted a quadratic effect on variables when the boron was applied near the reproductive stages. For the transgenic variety, the first-degree polynomial model presented the best fit, meaning that the higher the boron dose the better the physiological quality. The optimal boron application stage for producing high vigor seeds was R1 for both varieties. Four (4.0) kg ha-1 of boric acid is recommended for both varieties to produce high quality seeds.