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Plasmon diversity of 70 Houttuynia Thunb. accessions were investigated by using PCR-RFLP technology. The results not only revealed the interspecific, but also intraspecific plasmon variations within the genus Houttuynia. In total, 59 distinct organelle haplotypes were identified among 70 accessions, two in H. emeiensis and 57 in H. cordata. The average genetic similarities (GSs) values within H. emeiensis and H. cordata accessions were 0.986 and 0.950, respectively. The intraspecific GS value between H. emeiensis and H. cordata was 0.951. Two accessions of the new species H. emeiensis, W01-1 and W01-86, were very closely clustered together, but they could not be completely separated from H. cordata according to the cluster analysis. The results suggest that the classification of new species could be reconsidered. The level of genetic diversity between cultivated and wild groups in H. cordata was very low. The groups based on plasmon PCR-RFLP GS were little related with geographic distribution and chromosome number. We also discuss the phylogenetic relationship and phylogeographic information of the genus Houttuynia.