Based on the LTR sequences of dragon fruit (Hylocereus spp.) Ty1-copia retrotransposons,primers for IRAP were designed.The complete random orthogonal design L16(45) was used to optimize the IRAP-PCR system at four levels and five factors,namely,Mg2+,dNTP,Taq DNA polymerase,primers and DNA template.The results showed that the optimal system for IRAP amplification was 25 μL mixture containing 20 ng of template DNA,2.5 mmol/L MgCl2,0.10 mmol/L dNTPs,2.5 μL of 10×PCR Buffer,0.75 U of Taq DNA polymerase,0.25 μmol/L LTR primer.PAGE with 0.080 g/mL non-denaturing polyacrylamide gel could yield reproducible,clear and reliable bands,which facilitate the identification of dragon fruit germplasms,the elucidation of their genetic diversity as well as assessment of genetic variation.