Oyama sieboldii (K.Koch)N.H. Xia & C.Y.Wu is a rare species and has been listed as the national Ⅲ grade protection plants in China. The species is naturaly distributed in two different zones of forest vegetation, i.e., temperate deciduous broad-leaved forest (North of the Yangtze River) and warm temperate evergreen broad-leaved forest (South of the Yangtze River). The east region of China is one of the concentrated distribution areas of O. sieboldii, and also is the boundary zone of these two different vegetations. The genetic diversity and structure of eight wild populations of O. sieboldii, within two different vegetations from Eastern China, were analyzed by microsatellite markers. The results indicated that the genetic diversity of O. sieboldii in this region was relatively low (mean N_A=3.83, H_O=0.25 and H_E=0.40) and lower than its closely related species. The mean population size, diameter at breast height (DBH) and number of branch were not significantly different between populations from different vegetations. However, the genetic diversity of Dabieshan populations (mean H_O=0.18 and H_E=0.28), within the temperate deciduous broad-leaved forest, was significantly lower than that of the Southern Anhui populations (mean H_O=0.33 and H_E=0.51), within the temperate evergreen broad-leaved forest, and their genetic characters obviously differentiated from each other. The distinct population history might mainly explain the difference of genetic diversity between these two zones. The genetic diversity of young individuals was not significantly lower than that of the old individuals within each population. Therefore, we proposed that the populations in Dabieshan area and Southern Anhui area should be considered as two different evolutionary significant units for conservation, and an in situ conservation strategy should be taken as the main protecting measures at present, given that the regeneration ability of wild populations was normal and the genetic diversity of young individuals did not significantly decreased.