In order to clarify the biosynthesis of flavonoids in soybean seeds and to know the reason for flavonoids content variation among different soybean lines,PCR primers designed from the conservative domain of Chalcone Synthase (CHS) were used to isolate the CHS genes from soybean leaves by RT-PCR.As the results,three CHS genes involved in the biosynthesis of flavonoids were cloned out and named as GmCHS1,GmCHS2 and GmCHS3.After BLAST search against the soybean genome sequencing data base,the three CHS genes are identical with Gm08g11610,Gm05g28610 and Gm08g11520,respectively.Sequences alignment results indicated these three CHS genes shared 95%~98% identity on DNA sequence,and 98% identity on amino acids sequence.6 amino acids difference was found among these three CHS.Phylogenic analysis on the amino acid sequences of CHS from soybean and some other plants showed that the three soybean CHS were closely related to Senna tora and Phaseolus vulgaris.Gene expression analysis showed that the three CHS genes were differently expressed between two lines,which may be one of the major reasons leads to the variation of flavonoids contents in seeds among different soybean lines.