A method of capillary electrophoresis fingerprint was developed for evaluation of the quality of Arnebia euchroma ( Royle) Johnst. The samples were separated on a 50 μm × 40 cm uncoated capillary separation column at separation voltage of 25 kV with 100 mmol/ L borate buffer ( pH 8. 0) containing 25 mmol/ L SDS and 20% (V/ V) dehydrated alcohol as running buffer. The injection volume of sample was 0. 5 psi ×5 s and the detection wavelength was 214 nm. The results indicated that the samples of Arnebia euchroma (Royle) Johnst were well separated and detected in 35 min. With Shikonin peak as reference peak, 6 characteristic peaks of standard Arnebia euchroma (Royle) Johnst were determined. The quality discriminant analyses were accomplished for different kinds of samples named Arnebia euchroma ( Royle) Johnst that purchased from eight sources by means of characteristic fingerprint peak analysis, similarity evaluation and cluster analysis. This method had good reproducibility, and could be used for the quality control of Arnebia euchroma (Royle) Johnst.