Abstract: Persicae semen has been used for years as a traditional Chinese medicine to treat diseases. Because of their similar morphologies, Persicae semen was commonly inadvertently mixed with Armeniacae semen amarum (a toxic herbal seed). Development of a reliable method for discriminating Persicae semen from its adulterant is necessary to reduce confusion for the drug safety in clinical practices. This study evaluates the efficiency of high-resolution melting (HRM) combined with internal transcribed spacer 2 (ITS2) to analyze Persicae semen. Our findings show that HRM allows not only the identification of adulteration but also the quantification of the most common admixture. HRM sensitivity in adulterant detection was assessed through the analysis of mixing samples with different proportions of Prunus persica and Prunus armeniaca control. The results are presented as a linear regression with r of 0.96 and imply the capability of the method to detect adulteration. In particular, HRM detected seeds of Prunus persica in Prunus armeniaca at concentrations as low as 1%, and commercial products labeled as ‘Persicae semen’ were purchased from markets and could rapid authenticated by HRM analyses. This study is significant in the verification of the authenticity in the quality control of herbal medicine. In the near future, it is promising to be the main trend for identifying traditional Chinese medicinal materials.