Concentrations of 20 free amino aicds (FAAs) in a famous Tibetan medicine Gentiana dahurica was first investigated using 1,2-benzo-3,4-dihydrocarbazole-9-ethyl chloroformate (BCEOC) as the pre-column fluorescence derivatization reagent by reversed-phase high performance liquid chromatography (RP-LC). 20 amino acid derivatives (AAD) were separated on a Hypersil BDS C₁₈ column with a good baseline resolution within 65 min. Identification of 20 AAD was by online post-column mass spectrometry with an electrospray ionization (ESI) source. The validation of the method was examined by linearity, repeatability, and detection limits. Most linear correlation coefficients for AAD were >0.9990, and detection limits (at signal-to-noise of 3:1) were 6.5-178.2 fmol. There were 18 FAAs found in G. dahurica, of which seven FAAs were necessary to the people's health and related to the treatment of liver and gall disease. Variation of concentrations of the 20 FAAs showed geographical distribution difference among populations. Meanwhile a stable genetic diversity of FAAs composition of G. dahurica was also revealed at the species level. Results of the present study proved that the established method was rapid and reproducible for further separation and determination of FAAs in more medicinal plants.