To optimize the fluorescence labeling method of pilose anlter extracts (PAEs),PAEs was labeled by two fluorescent probes,fluorescein isothiocyanate (FITC)and Cyanine 5 (Cy5). Molecular weight of the two fluorescent dyes-labeled proteins was identified by sodium dodecylsulphate polyacrylamide gel electrophoresis(SDS-PAGE). The cytotoxicity of the two fluorescent probes was detected in PC12 cells. To observe their stability in gastric fluids and intestinal fluids, FITC and Cy5 labeled PAEs were dissolved in artificial gastric fluids and artificial intestinal fluids. There was no significant difference between the molecular weight of FITC labeled PAEs and Cy5 labeled PAEs. The fluorescence intensity of FITC labeled PAEs was slightly stronger than that of Cy5 labeled PAEs. Compared with FITC labeled PAEs, Cy5 labeled PAEs was not stable in artificial gastric fluids or artificial intestinal fluids. In conclusion, FITC is well suited to label PAEs for further identification or in vivo study.