Large yellow croaker (Larimichthys crocea) is one of the important economic fishes in China. Since 1970s, wild resources of large yellow croaker have been almost extinct due to overfishing. To solve the production problem, artificial breeding and cultured technology for large yellow croaker obtained successful breakthrough and the output of large yellow croaker was improved significantly. However, the quality of the cultured and wild large yellow croaker has great difference. In addition, the quality of cultured large yellow croaker from different environment is uneven. Therefore, the quality control methods for large yellow croaker are important for the development of large yellow croaker breeding industry. At present, fingerprint analysis has been widely applied to quality control systems of traditional Chinese medicines because of its advantages and popularity, and more chromatography and spectral methods including high-performance liquid chromatography (HPLC), gas chromatography, infrared spectrometry and mass spectrometry have been used for the fingerprint analysis, but HPLC fingerprint technology is rarely used in the quality control of aquatic products at present. In this paper, conditions for sample pre-processing, component extraction and HPLC analysis method were optimized, and a validated HPLC method coupled with cluster analysis, principal component analysis and discriminant analysis has been developed for the study of the HPLC fingerprint of large yellow croaker. Under the optimum conditions, muscles from cultured large yellow croaker (L. crocea) from Zhoushan and Fujian, L. polyactis, Nibea albiflora and Collichthys niveatus were freeze-dried and their chemical components were extracted using ethyl acetate. The chemical components from different samples were detected by Agilent 1260 DAD-HPLC on Thermo ODS-C₁₈ (250 mm × 4.6 mm, 5μm) eluted by acetonitrile-water (0.1% H₃PO₄) under the optimum conditions: Flow rate 0.5 mL/min, inject volume 20μL, and wavelength 210 nm. The HPLC fingerprints and mutual mode of large yellow croaker from Zhoushan and Fujian, L. polyactis, N. albiflora and C. niveatus were established using similarity evaluation system for chromatographic fingerprint of TCM (Version 2004). Similarity analysis results indicated that the similarity order of other samples to large yellow croaker from Zhoushan was large yellow croaker from Fujian > L.polyactis > N. albiflora > C. niveatus. The same species had the similar characteristic peaks of HPLC and could be clustered together, but cluster analysis could not distinguish large yellow croaker from Zhoushan and Fujian. In the principal component analysis, three principal components (PC1, PC2 and PC3) were selected and accounted for 80.36% of the original data. According to the results of principal component scores, the scatter diagram of 62 samples was drawn, and each sample was able to form distinct cluster in the principal component space, then the identification of large yellow croaker from Zhoushan and Fujian, L.polyactis, N. albiflora and C. niveatus was basically achieved. Based on the results of principal component analysis, PC1 was used to develop the discrimination function for distinguishing different type samples. The accuracy of the discrimination function was 98.4%. Therefore, the established method had good stability, precision and reproducibility, and it was also a very reliable and useful method for distinguishing large yellow croaker from different species and/or environment. On the whole, HPLC fingerprint combined with reasonable methods of mathematical statistics provides an effective method for large yellow croaker geographical origin traceability and species identification.