Abstract: The aims were to establish and optimize the amplification system of ISSR-PCR and further study the genetic diversity of wild Miscanthus sinensis populations. M. sinensis samples were collected from Jilin Province for the test. The influence of DNA template, Taq DNA polymerase, primer and annealing temperature on the PCR amplification was studied by the single factor test method. The results indicated that: 20 μL reaction system contained 40 ng template DNA, 0.4 mmol/L dNTPs, 0.6 μmol/L primer, Taq DNA polymerase 1.5 U. 10 ISSR primers with stable amplification bands and rich polymorphism for ISSR-PCR were selected, and the optimal annealing temperature was also found.