Abstract: In order to establish a stable, repeatable ISSR-PCR reaction system of Callicarpa kwangtungensis, the factors included the concentration of DNA template, dNTPs, Mg²⁺, primers and TaqDNA polymerase were studied through the single factor tests, orthogonal tests with the total DNA of C. kwangtungensis as experimental material. And the best reaction system of ISSR-PCR to C. kwangtungensis was established as follows: 0.25 mmol/L dNTPs, 1.00 U TaqDNA polymerase, 0.75μmol/L primers, 2.0 mmol/L Mg²⁺, 100 ng template DNA in 25μL reaction volume. PCR amplification program of better repeatability and stability was set up after a pre- degeneration 5 min at 94℃; degeneration 30 s at 94℃; annealing time 45 s, annealing temperature corresponds to each primer; extension 90 s at 72℃; 34 cycle from degeneration to extension in total; then extension 10 min at 72℃, finally conserved at 4℃. One hundred ISSR primers were used to screen the suitable primers with 4 samples from different populations of C. kwangtungensis, and 20 ISSR primers with good amplification were screened out.