Houttuynia cordata is an important medicinal and edible plant with abundant germplasm resources. How?ever， systematic studies on its genetic diversity have been relatively scarce in the past five years， particularly those utiliz?ing SSR molecular markers， which has hindered progress in variety improvement and resource conservation. To address this issue， this study employed both SSR and ISSR markers to analyze the genetic diversity of 140 H. cordata samples collected from 10 geographic populations across eight provincial-level administrative regions in China. The results revealed a high proportion of polymorphic loci， with SSR and ISSR markers showing rates of 94.20% and 93.20%， respectively， indicating high genetic diversity in H. cordata. Genetic differentiation and gene flow analysis demonstrated that the majority of genetic variation existed among populations， with genetic differentiation coefficients （GST） of 0.9508 （SSR） and 0.8903 （ISSR） and low number of migrants （Nm）， suggesting that geographic isolation may be the primary driver of population differentiation. Cluster analysis and principal component analysis （PCA） further revealed close genetic relationships between certain populations （e.g.， Mianyang and Chengdu in Sichuan； Maoming in Guangdong and Liuzhi in Guizhou）， while the genetic distances of other populations showed no obvious correlation with geographic distribution. These findings provide valuable insights for the conservation and breeding of H. cordata germplasm resourc?es.