Abstract: In this paper, a optimized SRAP-PCR amplification system for Phyllanthus emblica was established by the orthogonal design and single factor optimization. It suggested that each factor （template DNA、Mg2+、dNTPs、primers）had different effect on the results of PCR, and 50 ng template DNA, 2.0 mmol/L-1 Mg2+, 0.4 mmol/L-1 dNTPs, 0.3 μmol/L-1 primers in a total of 20 μL reaction solution could be able to amplified the most rich polymorphism and clear bands. The optimized SRAP-PCR system was tested on twelve Phyllanthus emblica germplasms and shown to be steady and reliable for molecular genetics research.