[Objective] The paper aimed to establish and optimize ISSR-PCR system of Houttuynia cordata Thunb according to the ISSR-PCR characters of Houttuynia cordata Thunb,which laid a foundation for the further study on population genetic diversity of Houttuynia eordata Thunb. [Method]The effects of ISSR-PCRs was examined with selected primers and concentration in the ISSR-PCRs,and the reliable ISSR-PCR systems for Houttuynia eordata Thunb populations was established through the analysis of the reasons for occurrence of differential bands and optimizing reaction conditions. [Result] The optimal ISSR-PCR system in Houttuynia eordata Thunb were significantly influenced by Taq DNA polymerase, annealing temperature,concentrations of Mg2+ and dNTP,etc. [Conclusion]The ISSR-PCR systems,which had characteristics of time saving,economic, simple and clear reliable abundant polymorphisms molecular markers and good reproducibility, and were suitable for studying population authentication and population molecular ecology of Houttuynia eordata Thunb.