Yunnan Province is one of the largest centers of genetic diversity of Oryza sativa L. in China, and in the world. Using a genetically representative core collection of 692 rice landraces from Yunnan, the genetic structure, differentiation, and geographic diversity of this rice germplasm were analyzed. The accessions were classified into different populations, according to the model-based structure analysis. Model-based populations were characterized through the reconstruction of a neighbor-joining tree, principal coordinate analysis, and the estimation of morphologic and SSR variations. Finally, the distribution of genetic diversity and differentiation among districts were studied. Seven model-based populations were identified on the basis of the structure analysis. This classification was partly consistent with Ting's 5-level taxonomic system. Differentiation between 2 rice subspecies is the most apparent, with a clearer differentiation between soil-watery ecotypes in japonica than in indica; however, differentiation among seasonal ecotypes in indica is clearer than in japonica. Cropping system and man-made restricted-growth environments could be considered to be the main forces driving the intraspecific differentiation of cultivated rice. It has been suggested that, because it possesses the highest genetic diversity and all the necessary conditions as a center of genetic diversity, the southwest region of Yunnan, encompassing Simao, Lincang, and Xishuangbanna districts, is the center of genetic diversity of Yunnan rice landraces.