To study the genetic diversity and differentiation of the three populations of Oryza rufipogon in Gaozhou, Guangdong Province, 30 pairs of SSR primers were used. The results indicated that: i) Only 20 pairs of SSR primers were polymorphic and 77 alleles were detected. The percentage of polymorphic loci (P) and the mean number of alleles per locus (Ap) were 66 7% and 4 05 respectively. ii) The total gene diversity of the three populations was 0 61, among which more than 75% was from the gene diversity within populations. iii) Though the coefficient of gene differentiation (G ST) was 0 2427, meaning that the genetic variability among populations was low, the dendrogram of the samples from all populations showed that the three populations were relatively separated with the coefficient increasing. Therefore, the genetic differentiation of the three populations definitely occurred but not obviously.