To identify Persicae semen amarum using DNA molecular identification,and establish classical PCR identification mesthod.The internal transcribed spacer (ITS) of nuclear ribosomal DNA of Persicae Semen and Armeniacae semen amarum were amplified and bidirectionally sequenced.ITS sequences were analysed by BioEdit.Specific identification primers were designed according to the ITS sequences of specific alleles,and PCR reaction system was optimized.Persicae Semen and Armeniacae Semen Amarum can be identificated by the specfic peimers G4-7 based on ITS sequences.In the condition's concentration is between 0.05-1 ng for a 25 μL PCR reaction,the best annealing temperature is 59 ℃.This method is well used for different DNA polymerases and different PCR instruments.The result showed that the 333 bp identification band can be amplified in Persicae semen,while it can not be amplified in Armeniacae semen amarum.It is confirmed that the PCR amplification system of specific alleles can be used to identify Persicae semen and Armeniacae semen amarum fastly and accurately.