Abstract: 【Objective】The objective of this study is to understand the genetic diversity of Puccinia polysora, the causal agent of Southern corn rust which is outbreaked recently in China, molecular techniques were used to analyze the genetic differences among the pathogen populations. 【Method】Seventy-two populations of P. polysora, collected from twelve provinces during 2011 and 2012, were amplified using eighteen polymorphic ISSR primers and the results were analyzed with software. 【Result】Seventy-two populations were clustered into ten branches at 81% Dice’s similarity coefficient, including two groups and five subgroups. There were some relationships in subgroup populations on collected loci and years and the higher genetic variations were tested among different populations. The higher genetic similarities were detected between Shandong and Anhui, Fujian and Zhejiang populations respectively, and the lowest similarities were between Hainan and others. The genetic relationship between provincial populations was lower based on the gene flow information.【Conclusion】There were higher genetic variations in populations of P. polysora, causal agent of southern corn rust, in China. Based on the molecular data, the pathogen did not complete the disease cycle in the field, and the population of P. polysora in Hainan was not the primary infection source in other provinces as well as the populations of P. polysora in Guangdong and Guangxi were not for summer-growing maize area. It was concluded that the primary infection source of P. polysora in mainland and Hainan island of China might come from other areas.

Key words: Southern corn rust , Puccinia polysora , genetic diversity , ISSR