The purpose of this study was to establish the optimal SRAP-PCR reaction system for potato, using the potato genomic DNA as a template and combining the single factor with the orthogonal experimental design, five factors including the concentrations of template DNA, Mg2+, dNTPs, Taq DNA polymerase and primers in SRAP-PCR reaction were optimized, then the optimal SRAP-PCR reaction system for potato was established. The results showed that ,the best SRAP-PCR amplification system is 60 ng template DNA, 1.5 mmol/L Mg2+ , 0.25 mmol/L dNTPs, 0.60 μmol/L each primer and 0.75U Taq DNA polymerase in a 20 μL reaction system for potato. And the order of each factor affecting the result of PCR is: Mg2+ > Taq DNA polymerase > DNA template > primer > dNTPs. The optimized system was verified by 6 potato DNA samples which obtained clear and stable polymorphic bands, it can be used to analyze the genetic diversity and construct genetic map of potato.