Germination of soybean seed is always arrested by chilling imbibitional stress, and this phenomenon is widespread in the plant seed kingdom, but has not been studied at molecular level. In this experiment, cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique was applied to isolate genes relevant to chilling stress (4°C) during soybean seed imbibition. Eight genes were found to be up-regulated and two were down-regulated during chilling stress respectively. Four up-regulated genes were selected to analyze the expression profiles during imbibition under chilling condition. It was demonstrated that the four genes were induced significantly by 4°C for 24 h, and decreased when the temperature was shifted from 4 to 22°C. GMCHI, a highly chilling stress-induced gene which responded to abscisic acid (ABA), polyethylene glycol (PEG) and NaCl, showed great stress-resistance according to published reports. Cos78 was identified to be induced by PEG. However, Cos66 and Cos36 transcription showed no change to ABA, PEG, and NaCl. From the characteristic of genes isolated from the embryonic axis, we concluded that soybean seeds have different pathways to adapt to various biotic and abiotic stresses by regulating many signal transduction pathways. Germination of soybean seed is always arrested by chilling imbibitional stress, and this phenomenon is widespread in the plant seed kingdom, but has not been studied at molecular level. In this experiment, cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique was applied to isolate genes relevant to chilling stress (4 ° C) during soybean seed imbibition. Eight genes were found to be up-regulated and two were down-regulated during chilling stress respectively. Four up-regulated genes were selected to analyze the expression profiles during imbibition under chilling condition. It was said that the four genes were induced significantly by 4 ° C for 24 h, and decreased when the temperature was shifted from 4 to 22 ° C. GMCHI, a highly chilling stress-induced gene which responded to abscisic However, Cos66 was found to be induced by PEG. However, Cos66 and Cos36 transcr From the characteristic of genes isolated from the embryonic axis, we concluded that soybean seeds have different pathways to adapt to various biotic and abiotic stresses by regulating many signal transduction pathways.