Abstract:In order to detect the diversity in populations of Blumeria graminis f.sp.tritici (Bgt), a orthogonal design and a single factor test, were used to optimize ISSR-PCR amplification system at different levels of five factors (Taq DNA polymerase, Mg2+, dNTP, primer and DNA template) and a suitable ISSR-PCR reaction system was established. The optimal annealing temperature of 20 primers was confirmed by gradient PCR and polymorphic primers were screened. Polymorphic bands of 33 isolates generated by primer BDB(CA)7 indicated that high diversity is conserved in DNA of Bgt. The dendrograms based on ISSR results and isolate virulence were also compared, showing that there is some relationship between DNA diversity and the diversity of the virulence.