In order to establish the optimal system of ISSR-PCR for Cyclobalanopsis gilva, with the genomic DNA of C.gilva leaves as material, single factor test and orthogonal experiment design were used to systematically test six parameters of ISSR-PCR which include template DNA, Mg2+, primers, dNTPs concentration, dose of Taq DNA polymerase and annealing temperature.Integrated analysis implies that the optimal reaction system of ISSR (20μL) is:20 ng template DNA, 2.5 mmoL/L Mg2+, 0.2 mmoL/L dNTPs, 0.2 μmoL/L primers and 1.0 U Taq DNA polymerase, if U...