Abstract: The use of random amplified polymorphic DNAs (RAPD) on the identification of crude drugs has a few special problems, e.g., the influence of the degree of degradation of DNA templates on the amplified products, the reliability of results by one or two primers and the application range of RAPD, etc., so the problems were discussed through researches on Herba Asari.In this experiment, the DNA of twenty-one samples from different locations and collected at different time were extracted. The suitable concentrations of DNA templates and the suitable primers were selected. After this, the DNA of these samples were amplified by RAPD. The results showed that the concentration and the degree of degradation of DNA templates, and the different sources of crude drugs affected the result of RAPD assay. Some suggestions were made to solve these problems, such as the selection of DNA templates concentration, the screening of suitable primers, and the use of contrast groups and cluster analysis. Furthermore, the application range of RAPD to the identification of crude drugs was discussed. All of these will provide the guide to the use of RAPD for the identification of crude drugs.