Abstract: To establish the optimal sequence-related amplified polymorphism(SRAP-PCR)system of Lpomoea aquatica,the concentrations of template DNA,10×PCR Buffer(including Mg2+),dNTPs,primer and Taq DNA polymerase,which maybe affect the SRAP-PCR reactions,were optimized by single factor test.The results showed that the optimal SRAP amplification system of lpomoea aquatica was established,which containing 80 ng template DNA,2.5mmol·L-1 10×PCR Buffer(including Mg2+),0.2mmol·L-1 dNTPs,0.4μmol·L-1primer and 1U Taq DNA polymerase.The molecular identification of two Lpomoea aquatica cultivars(‘Ben di'and ‘San cha')were conducted with the optimized SRAP marker system.7out of 25 SRAP primer combinations were selected to distinguish two Lpomoea aquatica cultivars and the amplification products were clear,bright and showed abundant polymorphism bands, which indicated that the optimized SRAP-PCR system could be applied in cultivars identification and genetic diversity research of Lpomoea aquatica.