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The objective of this study is to determine the genetic structure of RSB pathogenpopulations in southern China. Genetic diversity of the populations of RSB pathogen wereanalysis by RAPD markers. The isolates of 6 populations were recovered from the infectedsamples collected from Bao Shan in Yunan Province, Gao Yao in GuangdongProvince, Nan Chang in Jiangxi Province, Chang Sha in Hunan Province,Jing Zhou in Hubei Province and Fu Yang in Zhejiang Province, respectively.The dominant pathogen in these areas were R. solani AG-1 IA. A total of 193 loci weredetected by 16 RAPD primers among 180 isolates, of which 169 loci were polymorphic, thepercentage of polymorphic loci was 87.56％, The Shannon information index and Neisgene diversity was 0.5269 and 0.3486 at species level, respectively, and 0.4625 and 0.3077at population level, respectively. Total genetic diversity of 6 populations was 0.3486, andgenetic diversity within populations was 0.3077. The coefficient of gene differentiation andgene flow among the populations were 0.1120 and 3.7619, respectively. The genetic identitybetween populations were higher, while genetic distance between populations were lower.AMOVA demonstrated that lower genetic differentiation occurred among populations. Therewas no significant correlation between genetic and geographic distance among populations.