Abstract: We studied variation in 37 simple sequence repeats (SSRs) in 2 populations of common wild rice Oryza rufipogon from Qionghai and Sanya in Hainan. SSRs had more genetic variability in the Sanya than in the Qionghai population. The genetic identity and distance between the 2 populations were 0.6385 and 0.4486 cM, respectively. The result of Wright’s FST showed that 37 SSRs had moderate genetic differentiation within the Qionghai and Sanya populations, with an FST=0.3909,which was mainly caused by lower gene flow, with an Nm=0.3895.