Four different DNA extraction methods were used to obtain genomic DNA of Synchytrium sp.from the sori isolated from Pueraria lobata(Willd.) Ohwi,P.thomsonii Benth.,P.montana(Lour.) Merr..The modified method using benzyl chloride is the most efficient one to extract genomic DNA.rDNA-ITS can be successfully amplified directly from a single sporangium by PCR.The ITS sequence length of the isolates from P.lobata and P. thomsonii are 856 bp and 907 bp respectively shared 92% sequence similarity; the ITS sequences from P.montana are 1 148 bp,with 54% and 55% sequence similarity to the isolates from P.lobata and P.thomsonii respectively.The results indicated that the isolates from P.lobata and P.thomsonii are different varieties of the same species or two closely related species and the isolates from P.montana are another species of Synchytrium,or a more distantly related species.