Abstract: A orthogonal design was used to optimize SSR amplification for Cryptomeria fortunei in five factors:Mg²⁺,DNA template,Taq DNA polymerase,dNTP, primer. The results were shown as follows:(1)A suitable 10 μL SSR reaction system contained Mg²⁺ 2.0 mmol/L, each of four dNTPs 0.15 mmol/L, primers 0.3 μmol/L, Taq polymerase 0.5 μmol/min, DNA template 20 ng.(2)Twenty-six SSR primers were screened from 106 primers existing in Cryptomeria,which had high polymorphism and stability.(3)The best annealing temperature of twenty-six SSR primers were optimized. The results provided references for genetic diversity research of C. fortunei using SSR marker.