Abstract:Genetic diversity of 34 isolates of Sporisorium reilianum from main corn producing areas in China was analyzed by UP-PCR (universally primed PCR), ISSR (internal simple sequence repeat) and AFLP (amplified fragment length polymorphism). The results showed that 9 primers of UP-PCR, 11 primers of ISSR and 22 primers of AFLP generated 113, 72 and 293 polymorphic bands, accounted for 91.15%, 84.7% and 83.27% of total bands respectively. These molecular markers revealed the genetic diversity of the strains tested, and there was no significant correlation between variation and region. The correlation between UP-PCR and AFLP, which was 0.698, was higher than that between UP-PCR and ISSR, or ISSR and AFLP, which were 0.659 or 0.633 respectively, by the analysis of genetic similarity coefficient matrix from three kinds of molecular markers. The UP-PCR technique was suitable for the genetic diversity analysis of S.reilianum in view of the level of polymorphism, stability and operability. In addition, there was a certain correlation between the groups divided by UP-PCR, ISSR and AFLP molecular markers and the pathogenic types identified by host identification, coincidence rate were 50.0%,60.0%,and 47.6% respectively.