OBJECTIVE： To establish HPLC fingerprint of Capsicum annuum，and to conduct cluster analysis and principal component analysis. METHODS： HPLC method was adopted. The determination was performed on Agilent C18 column with mobile phase consisted of methanol-0.2％ phosphoric acid solution （gradient elution） at the flow rate of 1.0 mL/min. The detection wavelength was set at 235 nm， and column temperature was 30 ℃. The sample size was 15 μL. Using capsaicin peak as reference， HPLC fingerprints of 15 batches of C. annuum from different production areas were determined. The similarity evaluation of common peaks was evaluated by using the TCM Chromatographic Fingerprint Similarity Evaluation System （2004 A edition） to confirm common peaks. Cluster analysis and principal component analysis were performed by using SPSS 19.0 software. RESULTS： The similarities were more than 0.95 in HPLC chromatograms of 15 batches of C. annuum. There were 12 common peaks. Its HPLC fingerprint was in good agreement with that of control fingerprint. 15 batches can be divided into three sub-categories as S1， S3-S5， S7， S9-S13 sub-categorie， S2， S14， S15 sub-categorie and S6， S8 sub-categorie. Through the principal component analysis， the cumulative contribution rate of 4 main component factors was 94.093， and comprehensive score of S5  was the highest with the best quality. CONCLUSIONS： Established HPLC fingerprints， cluster analysis and principal component analysis results can provide reference for the quality control of C. annuum.