Abstract: OBJECTIVE To establish the HPLC fingerprints of Cynomorium songaricum Rupr (CSR) from different areas, and determine the content of two flavonoids. METHODS HPLC-DAD method were developed to establish fingerprints for CSR, and determine the contents, performanced on the Dikma Spursil C₁₈(4.6 mm×250 mm, 5 μm) and methanol-0.2% formic acid water as the mobile phase for gradient elution. Similarity evaluation system for chromatographic fingerprint of traditional Chinese medicine (2012 edition) was used to confirm the common peaks in 12 batches of samples and evaluate the similarity. SPSS 21.0 statistical software was used to make cluster analysis(CA) and principal component analysis(PCA) for the HPLC fingerprint. RESULTS The common mode for CSR fingerprint was established, the similarity was >0.90 in 12 batches of CSR, and 22 common fingerprint peaks were identified. And the contents of catechin and phloridzin were determined, the average of contents were 0.320, 0.057 mg·g^-1, respectively. Different batches of samples could be classified into four groups by using CA, reflecting the quality characteristics of 12 batches of CSR in different areas. Five principal components with a cumulative contribution rate of 89.349% were screened by using PCA to obtain four chemical compositions that could determine the quality of CSR. CONCLUSION The HPLC fingerprint combined with content determination, CA, PCA methods can objectively, effectively, fully for quality evaluation of CSR.