Objective To establish the analytical method for the fingerprint of Flos Chrysanthemi by HPLC and estimate the quality of Flos Chrysanthemi in various species from different habitats. Methods The gradient elution mode was applied in chromatographic separation,data can be treated by competitive layer neural network(NN) and pattern recognition be made for Flos Chrysanthemi samples of various species from different habitats.Results The analytical method of fingerprint for Flos chrysanthemi by HPLC was established,samples can be classified into five categories according to the recognition result.Conclusion The established fingerprint can be used for the identification and quality control of Flos Chrysanthemi.