The core germplasm of H.cordata Thunb was established by classifying 16 kinds of Houttuynia cordata Thunb germplasm which were collected from 11 villages and towns in Huaihua region of Hunan province according to their locality, their proportion and their diversity index in each group. The result of the test of genetic diversity index of 24 phenotypic traits indicated that a primary core germplasm accounted for 15%~20% to the collectivity materials; the character conformities were above 84% and the other characters range ratio were above 80% except for the diameter, branch number of overground, the branch number and node length, the leaf length and petiolar length. All of these showed that the established core collection can preferably represent H.cordata Thunb gerplasm.