Abstract:In order to study the genetic diversity of Horsfieldia pandurifolia from Xishuangbanna and Lincang of Yunnan province, genetic diversities of 56 samples from 8 populations were tested by AFLP markers. The results showed that a high genetic diversity existed in H. pandurifolia, with the percentage of polymorphic sites were 75.16% at species level, and 36.20% at population level. Moreover, a high level genetic variation (75.45%) within the population was detected through AMOVA analysis, but only existed 24.55% between populations. Analysis of correlation between geographical distance and genetic distance showed that there was positive correlation (r=0.1197，p=0.3210) among the populations，but it was not significant. Based on the UPGMA clustering analysis of the coefficient of genetic similarity, the 8 populations were divided into 3 groups at a similarity coefficient threshold of 0.951. On the basis of these results, the strategy was proposed for the conservation germplasm and laid a foundation for the development and sustainable development of H. pandurifolia.