Abstract: We established an advanced SRAP-PCR reaction system for Chinese Antique Lotus and American Lotus using a single factor experiment with five impact factors,including DNA template,Mg²⁺,dNTP mixture,Taq DNA polymerase and primer.The 10 μL reaction mixture contained 50 ng of genomic DNA template,1 μL of 10×Buffer,2 mmol/L of MgCl₂,0.20 mmol/L of dNTP,0.75 U of Taq DNA polymerase,and 0.8 μmol/L of primers.To test the stability of the optimized SRAP-PCR system,the PCR was further amplified in the core-collection of flower lotus with 88 cultivars using 16 primer pairs.A total of 183 clear bands were obtained throughout all materials,of which 165 (90%) bands were polymorphic. Therefore,the established SRAP reaction system for lotus was reliable.The results provided technical support for evaluating genetic diversity as well as constructing genetic linkage maps and molecular marker-assisted breeding of lotus.