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Surface Enhanced Raman Scattering (SERS) combined with Thin Layer Chromatography (TLC) has been used for studying characteristic spectrum of molecules in situ in micrograms samples. There are very few report for applying the SERS-TCL method in the study of the effective ingredients of Chinese traditional herbs. Coptis Chinensis France is an often-used clinic Chinese traditional medicine. Its main effective components include berberine and so on, which have antibiotic very wide and also have curative effect on improving the functions of heart vascular cycles. Therefore the concentrations of berberine are very important for the quality control of the medicine. In this work, the ethanol extract of Coptis Chinensis France was first separated by TLC, the SERS was then measure directly after dropping silver gel on the separated spots. The method can be used for the finger print analysis of the berberine. 3 microL of alcohol extract of Coptis Chinensis France with total alkaloids concentration of 1.0 mg.mL was placed on silicon GF254 TLC plate. The sample was separated by developing solvent of n bulanol-Acitic acid-H2O (7:2:1 V/V). The positions of berberine in the sample were confirmed by the standard alkaloid solutions. The Rf values for berberine are 0.29. The silver gel was used as surface enhanced substrate and placed on the separated berberine spots. FT-SERS was measured directly by a Nicolet FT-Raman 910 spectrometer. Berberine belong to isoquinoline alkaloids. His structure can be found in reference. The date of spectrum of berberine can be seen that the band at 1,396 cm-1 due to Ar-OCH3 deformation vibrations was greatly enhanced, indicating that the molecule was absorbed on silver gel strongly through lone-pair electron in Ar-OCH3. The ring stretching mode occurring around 1,548 cm-1 represents isoquinoline ring in the molecule. The band at 727 cm-1 due to CH (ring) deformation vibrations was also enhanced.