Persicae Semen (PS), a traditional Chinese medicine, has been widely used for the syndrome of blood stasis in China since the Eastern Han Dynasty. In the present study, we developed an HPLC-UV fingerprint analysis method for the quality control of PS. The HPLC fingerprint was performed on Shimadzu Inertsil C18 column (4.6 mm x 250 mm, 5 microm) at 35 degrees C. The mobile phases were composed of acetonitrile and water using a gradient elution. The flow rate was 1.0 mL x min(-1), and the detection wavelength was set at 210 nm. The fingerprint method was validated according to the Guidelines for Traditional Chinese Medicine Injection Fingerprint, and applied to determine 41 batches representative herbs collected from Xinjiang of China. The chromatographic peaks were characterized by UPLC-Q-TOF-MS, and nine of them were identified by comparison with the literature and/or reference standards. In order to classify and assess the samples, hierarchical clustering analysis and partial least square discriminant analysis were performed based on the common chromatographic peaks, and the samples were geographically classified into two classes, with six chemical compounds as classification markers which were significantly different between the two classes (P < 0.05).