Abstract: Total genomic DNA was extracted from Polygonum capitatum by a modified cetyltrimethyl ammonium bromide (CTAB)protocol. The purified products of PCR amplifications were directly sequenced, associated with rDNA ITS sequences in triplicate, using consensus primer pairs. Nucleotide sequence analysis, phylogenetic tree and homology were performed with Clustal X software and DNAMAN programme based on DNA ITS sequences. The results indicated that the sequences of rDNA ITS were 661~666 bp in P.capitatum, and 13 variable sites, mainly concentrated in the ITS1 and ITS2 area. We argued that rDNA ITS sequences could be applied to explore molecular identification to determine the sampled eco-geographic origins in P. capitatum.