Abstract: Based on the stage definitions of seed germination and post-germination growth, we investigated the variations of contents of three major flavonoids during the two stages in Astragalus membranaceus and its variety of mongholicus. Besides, in order to understand how the variations were induced, the transcriptions of pathway enzyme involving in flavonoid biosynthesis were profiled. The contents of flavonoids increased during the two stages in both A.membranaceus and the variety. With the detection of gene transcriptions of the pathway enzymes, only the enzymes in upstream of the pathway contributed to the increase of flavonoids in the variety of mongholicus during the germination, whereas it was that almost all the pathway enzymes were involved in A.membranaceus. The transcriptions of pathway enzymes regulated the accumulations of flavonoids during post-germination growth, selectively with a pattern of time delay.