Oryza rufipogon Griff, which is recognized as the genetically closest wild species of cultivated rice (O. sativa L.), is an important resource valuable in rice improvement. In this study, 1777 O. rufipogon germplasm accessions, which were collected from China, were subjected for the genetic diversity analysis of five important agronomic traits including heading date, anther length, grain length, grain width and 100-grain weight. The principal component and variance analysis showed an abundant diversity, with the coefficient of variations on heading date, anther length, grain length, grain width and 100-grain weight of 0.06, 0.17, 0.07, 0.09 and 0.16, respectively. The diversity index of five phenotypic traits was 0.69, 0.72, 0.70, 0.65 and 0.71, respectively. By principal component analysis, the first and second components were found to be mainly associated with yield traits, with the cumulative contribution rate of 83.31%. The third principal component was mainly related to the heading date, with the cumulative contribution rate of 11.69%. The common wild rice collection was classified into three clusters, which were roughly explained by the collection sites. For examples, the samples of cluster1 were mainly collected from Jiangxi and Hunan; the samples of cluster2 were mainly collected from most areas of Guangxi and Guangdong and Fujian; the samples of cluster3 were mainly collected from Hainan and the southern part of Guangdong (Zhanjiang). The analysis of variance of five important agronomic traits based on geographical location showed that the variation of anther length, heading date and grain length among different geographical groups accounted for 69.09%, 57.98%, and 77.56% of the total variation, and Grain width variation accounted for 6.20%. Variations in anther length, heading date, and grain length played a decisive role in diversification among common wild rice geographic groups.