Abstract: Abstract：The method for extraction genomic DNA from Baphicacanthus cusia(Nees)Bremek and some essential factors affecting the result of RAPD-PCR were investigated in the paper.PVP andβ-mercaptoethanol were added to lyses buffer in order to inhibit oxidation of polyphenol,high concentration of salt solution and elution for many times were used to remove polysaccharide, using above methods ,high quality DNA of Baphicacanthus cusia(Nees)Bremek could be obtained. Based on the high quality genomic DNA,some reaction conditions of PCR for RAPD were optimized.The results showed that the RAPD-PCR system with TaqDNA polymerase 1.25U, dNTP 0.25mmol/L, Mg2+ 2.5mmol/L,genomic DNA 50ng and random primer 1.0μmol/L in 20μl solution was suitable for Baphicacanthus amplification reaction.