Abstract: In this paper, orthogonal design to SRAPPCR system for Camellia oleifera cultivar Dabieshan 2 and Ganxing 46 was conducted with the primers combination of Me5 and Em8. Orthogonal designdirect analysis and variance analysis were applied to optimize SRAPPCR amplification system in 4 factors such as Taq DNA polymerase, Mg2+, dNTP and primer. Template DNA was also analyzed by the single element test. The results indicated that an optimal reaction system (20 μL)of SRAPPCR system was established: 120 μmol/min Taq DNA polymerase 125 mmol/L Mg2+, 0.15 mmol/L dNTP, 0.60 μmol/L primer, 60 ng template DNA and 2 μL 10 buffer(Mg2+ free). And, the order of each factor levels affected on the result of SRAPPCR was dNTP, Mg2+, Taq DNA polymerase and primer.