Abstract: AIMTo discuss the genetic diversity of the germplasm resources of Herba Houttyniae on molecular level. METHODSThe genetic diversity of 92 Houttuynia Thunb. accessions were tested by RAPD markers. RESULTSOf 34 10-mer arbitrary primers, 32 (94.1%) were found to amplify polymorphic products. A total of 200 products were amplified of which, 93.5% products were found to be polymorphic. 5.8 polymorphic bands were amplified by each polymorphic primers on the average. The average genetic similarity (GS) within Houttuynia cordata Thunb. and Houttuynia emeiensis Z.Y. Zhu et S.L. Zhang accessions were 0.521 and 0.572, respectively. The GS between them was 0.517. The degree of similarity of Houttuynia emeiensis Z.Y. Zhu et S.L. Zhang accessions and Houttuynia cordata Thunb. cytotype which had the chromosome number of 36 was the highest, with an average of 0.530. The genetic diversity of cultivated groups was higher than that of wild ones. The results of cluster analysis by using UPGMA method showed that all the tested accessions can be differentiated by RAPD markers, and classified as 14 groups. Of which, 62 accessions was classified as one group. The results also showed that the genetic diversity in Herba Houttyniae based on RAPD GS was correlated with geographic distribution. CONCLUSION(1) There actually existed much genetic diversity on molecular level among the germplasm resources of Herba Houttyniae. (2) RAPD markers could be effective tools to construct DNA fingerprintings of Herba Houttyniae. (3) The genuieness of Herba Houttyniae was related with the environments. However, it was affected by genetic facters in more degree.