Abstract: The research established a cDNA-AFLP analysis system which suited Paeonia lactiflora seed by using hybrid seeds of P.‘Fenyunu’and P.‘Fenzhonglou’as materials and optimizing the important factors which affect the reaction of cDNA-AFLP. In addition，we made a preliminary analysis on the expression difference of gene under the conditions of before and after breaking epicotyl and hypocotyl dormancy. The results indicated that total RNA was isolated from Paeonia lactiflora seeds using the RNAprep Pure Plant Kit according to the manufacturer’s instruction. Doubled-stranded cDNA was digested completely with EcoRⅠand MseⅠat 37 ℃ for 4 h and at 65 ℃ for 20 min. The ligated products should be diluted 10 times with sterilized distilled water for the pre-amplification. Then relatively clear and differentiable bands were obtained after the pre-amplified products were diluted 10 times，and 5 μL were taken as a template for selective amplification. About 3 700 differential bands were visualized between before and after breaking hypocotyl dormancy and about 1 600 differential bands were visualized between before and after breaking epicotyl dormancy.

Key words: Paeonia lactiflora, seed, dormancy, cDNA-AFLP