Three natural populations of ( O. rufipogon ) in Yuanjiang are distributed at the top of a hill (780 m) and separated about 100 m each other. To investigate the genetic diversity of the populations, 30 SSR primers were used and 77 alleles were detected. The results indicated that the genetic variability of the wild rice in Yuanjiang is relatively high (Ap=2 6, Hs=0 77) and the coefficient of gene differentiation (G ST ) was 41 08%, meaning that the genetic variability among populations was high and all populations should be conserved separately. Moreover, even in the same population, individuals being distributed in different micro environments have different genetic backgrounds. Therefore, random sampling with artificial selection is necessary for ex situ conservation.