To explore genetic diversity and population structure of common wild rice of Guangxi, we investigated patterns of genetic diversity in a large collection comprising 4173 common wild rice germplasms from 14 cities in Guangxi using 64 molecular markers on 12 chromosomes of rice. The result showed that a total of 1180 alleles were detected with a mean of 18.4375 alleles per locus. Mean Shannon index was 0.64 and mean Nei index was 1.7367. The genetic diversity of common wild rice in Guangxi showed very abundant. A core collection representing the genetic diversity of these germplasms was identified using priority preservation-stepwise cluster method. Thus, a core collection bank of common wild rice including 351 germplasm, which accounted for 8.41% of total germplasm, was constructed.