Abstract: Molecular fingerprints map is very important to the identification, breeding and intellectual property right protection of Camellia japonica cultivars. To screen applicable SSR primers and the corresponding optimizing reaction system for the construction of SSR-PCR fingerprints map, graded annealed temperature and orthogonal diagram experimental design were employed to evaluate the reaction conditions for 4 pairs of SSR primer. The results showed that: clear and unambiguous electrophoresis bands with designed size of amplified production presented only with primers MSCjaF25 and MSCjaF37 under the amplifying condition of annealing at 52.9℃, 1.2 mmol/L Mg²⁺, 0.2 mmol/L dNTPs, 0.5 U Taq DNA polymerase, 0.2 mmol/L primers and 40 ng DNA template in 10 mL reaction system and annealing at 58.2℃, 0.8 mmol/L Mg²⁺, 0.1 mmol/L dNTPs, 1.0 U Taq DNA polymerase, 0.3 mmol/L primers and 40 ng DNA template in 10 mL reaction system, respectively. Amplifying of 12 Camellia japonica cultivars using primers MSCjaF25 and MSCjaF37 made pure confirmation to the repeatability and stability of these optimized reaction conditions. Further analysis revealed that screening more SSR primers had been the facing challenge for molecular fingerprints map study on Camellia japonica cultivars.