The Tropic of Cancer in China has been recognized as the center of Oryza rufipogon with abundant superior genes such as resistance to diseases and pests.To provide information for the conservation of O.rufipogon in this area,342 individuals from 13 populations near the Tropic of Cancer in Laibin City,Guangxi Autonomous Region,were collected and studied for the genetic diversity and population structure with 26 SSR primer pairs which were distributed among the genome of rice.The results indicated that:(i) Relatively high level of genetic variation was detected both at species(A=9.154,Ae=4.446,I=1.547,He=0.671) and population levels(P=95%,A=4.219,Ae=2.394,I=0.905,He=0.476) comparing to previous studies on O.rufipogon.(ii) The genetic differentiation(Gst=0.30) suggested that 30% genetic variation existed among populations,meaning that most variation happened among the individuals within populations.(iii) The cluster analysis showed that genetic identity among populations was negatively correlated with geographical distance,consistent with the isolation by distance model for the isolation populations.Based on the above results and the conservation actuality of O.rufipogon in China, it could be concluded that population G13 and G06 should be given priority for in-situ conservation.