【Objective】 To confirm genetic diversity distribution center of common wild rice，Oryza rufipogon Griff., in Guangxi, and construct the core collection which will provide a reference for protecting and utilizing wild rice resources in Guangxi. 【Method】 A total number of 623 common wild rice resources from Yujiang River Basin，Hongshui River Basin，Nanliujiang River Basin and Guibei Mountain were used to study the genetic diversity with 24 SSR markers. The stepwise cluster analysis was used to construct 10% and 5% core collections of common wild rice in Guangxi. 【Result】There were 114 alleles to be detected at 24 SSR loci. The number of alleles per locus (A) was 4.75, the average number of effective alleles (A_e) was 3.000 1, the Shannon-weaver information index (I) was 1.180 1 and the average expected heterozygosity (H_e) was 0.638 8. The order of genetic diversity of 9 regional populations was Yongning (YN) > Lingui (LG) > Fusui (FS) > Rongxian (RX) > Guigang (GG) > Pingnan (PN) > Gupeng (GP) > Wulitang (WLT) > Bobai (BB). The order of genetic diversity of four regions was Yujiang River Basin>Guibei Mountain > Nanliujiang River Basin > Hongshui River Basin. There were 31 copies belong to 5% core collection，including 14 copies of Yongning population and 12 copies of Fusui population which accounted for 5.76% and 18.75% of analyzed samples respectively. 【Conclusion】The genetic diversity center of Guangxi common wild rice is Yujiang River Basin. Wild rice of Yongning is widely distributed and presents various types. Wild rice of Fusui shows great rich genetic diversity. Yongning and Fusui regional populations，which are main sources of the core collection samples，are considered to be the most important populations of Guangxi common wild rice，and should be paid particular attention to their protection and exploitation.