To determine the role of O. rufipogon populations in Yunnan Province in the origin of cultivated rice, 27 SSR primers were used to analyze the genetic diversity of O. rufipogon populations from Yunnan and the neighbor areas. The analysis result indicated that the genetic diversity of O. rufipogon from other provinces of China and Southeast Asia were higher, while that of Yuanjiang materials was the lowest. The relationship analysis results indicated that there was obvious genetic structure between O. rufipogon in Yuanjiang population and Jinghong population. The population from Yuanjiang County had a closer relationship with those from China; while samples from Jinghong County and Myanmar had the closest relationship. All the results inferred that O. rufipogon from Yunnan might be the bridge type between those from China and Southeast and South of Asia, which may provide the scientific reference for the theory “Cultivated Rice Originated in the Area from India-Assam to China-Yunnan”.