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Rubber tree powdery mildew, caused by the obligate pathogen Erysiphe quercicola, is a major threat to rubber tree plantations worldwide. To investigate the temporal changes in the population structure of E. quercicola, diseased samples were collected at three disease epidemic stages (overwinter, early epidemic and late epidemic) from three counties in Hainan, China. Population structure was assessed using 16 polymorphic microsatellite markers. Both permutational multivariate analysis of variance (PERMANOVA) and analysis of molecular variance (AMOVA) indicated that there were significant differences among the population structure of E. quercicola at different epidemic stages. Furthermore, the late epidemic populations had higher genetic diversity than the other two stages. Discriminant analysis of principal components (DAPC) and STRUCTURE analysis showed that E. quercicola samples grouped into four clusters. One of the clusters included only samples from the late epidemic stage, while the other three clusters included samples from all three sample stages. Further analysis confirmed that there were significant (p= 0.001) genetic differences among these four clusters. As the teleomorph stage of E. quercicola has not yet been reported on rubber tree, these findings suggest that the epidemic of rubber tree powdery mildew is not only established by local inoculum sources, but also may be by inoculum drifting from other plantations or through host jumps from other hosts