Object To analyse genetic polymorphism in DNA level of three species and determine them in molecular level by using of the optimization of Citrus medica cv. sarcodactylis (Noot.) Swingle RAPD reaction.Methods RAPD reactions were performed under the following conditions:template DNA 10～100 ng/?L, 3.0～5.0 mmol/L MgCl 2, 200 ?mol/L dNTP,0.2 ?mol/L 10 mer Primer, lunit Taq Polymerase/25 ?L reaction volume.Results Twelve efficient and stable primers were selected from 38 primers. Phenograms were constructed by using genetic distance UPGMA method. Based on the results of the RAPD analysis and on a review of morphological characterisitic, C. medica cv. sarcodactylis species BAIHUAQINGPI could be used as BAIHUABAIPI in three species, there were some special amplified bands in every RAPD reactions from different species. Conclusion This method could serve as an easy and highly efficient method for C. medica cv. sarcodactylis genetic polymorphism and molecular identification of species.