The objective was to evaluate the effects of different harvest times and storage periods on the physiological quality of amaranth seeds of the cultivar BRS Alegria. The quality of the seeds was evaluated in three moments of harvest, with intervals of 20 days and the period of storage, in four moments, at the moment of the harvest and other three evaluations in intervals of 30 days, in addition to evaluations of the isoenzymatic expression after two years of seed storage in a cold chamber. Variations in the physiological quality of amaranth seeds were observed at different harvest times and storage periods. Noting an important reduction in the physiological quality of the seeds when stored for 90 days.