To develop a HPLC-DAD-ESI-TOF/MS analysis method for the determination of gentiopicroside and loganic acid in Radix gentianae samples and for the research of their fingerprints.The samples were extracted using ASE for 10 min under 100 ℃ and 9.65 MPa,and divided into water phase and chloroform phase and analyzed them with HPLC-DAD-ESI-TOF/MS method respectively.Based on this method,the HPLC fingerprints of Radix gentianae were established.Comparing the spectrogram and mass spectrum of the chromatogram peak with the reference value,three compounds in water phase were identified as gentiopicroside,asafetida acid and loganic acid.There is no report of the compounds in chloroform phase.The content of gentiopicroside and loganic acid in samples of different groups were determined,separately.The fingerprints were compared by the software of the similarity evaluation system for chromatographic fingerprint.The water phase fingerprint congruence coefficients of samples from six different areas were above 0.90,however,the chloroform phase fingerprint congruence coefficients were within 0.62-0.99.This method can be used for determination of potent component in Radix gentianae and its quality control.Radix gentianae from different producing areas have the largest diversities,and the diversities embodied in the content of chloroform phase compounds.