Abstract: Optimization on SSR reaction system is the fundamental step in SSR genetic map construction for Carya cathayensis. The systematic experiments on dosage of Taq DNA polymerase, dNTP concentration, concentrations of the primer, Mg²⁺ and template DNA and other factors were carried out to screen the optimal reaction system. It was indicated by the results that the optimal reaction system of SSR for Carya cathayensis was 30 μL of total reaction volume containing 600 ng of template DNA, 1×PCR Buffer, 2.0 units of Taq DNA polymerase, 0.22 mmol/L of dNTP,1.0 mmol/L of Mg²⁺ and 0.13 μmol/L of primer.