Abstract: The genetic structure of 217 individuals from seven natural populations of oryza rufipogon Griff. in Gaozhou was analyzed by use of 32 pairs of simple sequence repeat(SSR) primers. The populations differed in genetic structure but were also similar to some extent because of genetic introgression. The genetic diversity index of all populations(Ht) was 0.65; the diversity within populations(HS=0.431) was slightly higher than that among populations(DS=0.392), and the coefficient of genetic differentiation(GST) was 0.611. Thus, the genetic differentiation of o. rufipogon Griff. in Gaozhou was caused by differentiation within and among populations. The level of genetic similarity was high among populations A, B, and E and among populations D, F, and G; the genetic difference between population C and other populations was large. Considering the geographic distributions of the populations with the above results, population C, with the minimum genetic differentiation, and populations B and E, with the maximum genetic diversity, should be conserved before others.