Rice landrace is the main part of resources in rice (Oryza sativa L.). It has abundant genetic diversity and excellent characters that the current widely-planted variety has not. It is the indispensable resources to breed and study the origin and evolution of rice species. Inter-varietal genetic diversity were attended; however, intra-varietal genetic heterogeneity were not. Twenty-four SSR markers were used to evaluate the intra-varietal heterogeneity of 3 rice landraces that has been continuously planted generation to generation in Yuanyang terraces of Yunnan Province, China. A total of 117 SSR alleles were revealed, and the Shannon's information index of 3 populations were Hongjiaolaojing (0.5911) > Baijiaolaojing (0.4875) > Yuelianggu (0.3070). The results of this study showed that they have abundant intra-varietal heterogeneity in 3 rice landraces. The contribution rate of genetic heterogeneity among plants individual is higher than among populations.