In the present study, the genetic diversity of microsatellite sequence (CT)n and intron 1 G/T in Wx Gene were determined for 90 individuals in the natural population of O.rufipogon from Yunjiang of Yunnan Province , 9 wild rice lines of O.rufipogon, and O.longistaminata from Dongxiang of China ,India, Indonesia, Cameroon and Cote Divoire. In the loci of the microsatellite sequence (CT)n and intron 1st G/T in Wx gene, all of individuals from the natural population of wild rice in Yuanjiang were homogenetic, whose intron 1 G/T were base G the band type of microsatellite sequence (CT)n wassimilar to one of the local indica cultivars from Yunnan.