Grain color distinguishes between the pigmentation of the outer layer of the kernel. It is known that environmental factors affects the production of anthocyanins and abiotic stresses like high light intensity, low temperature, high salinity and/or drought stress, and others increase their amounts. After 7 days the germination rate between yellow and dark-purple seeds were almost the same with and without stress (100% yellow seeds under stress and without stress germinated, 93.3% under stress and 96.6% without stress of purple seeds germinated), even though at the final stage the germination was almost the same, we can conclude base on our observations that the germination takes place at a different rate. We think that this might be related to the seed color, since the germination of purple seeds under salt stress started earlier than the yellow ones, until both reached the same point. The antioxidant activity was higher in seedlings from dark-purple seeds than the yellow ones, and they were higher under salt stress than without it, supporting our hypothesis that the purple color in wheat seeds works as a protection under salt stress. Furthermore, the qRT-pCR showed that some genes related to the flavonoid pathway were expressed or had more expression in the seedlings from dark-purple seeds than yellow ones.