A capillary zone electrophoresis method was developed for simultaneous determination of nine flavonoids, including two rare flavonols, in Tibetan medicine Anaphalis margaritacea. Baseline separation was performed at pH 9.6 with 25 mM Na(2)B(4)O(7) and 10 mM NaH(2)PO(4) buffer solution, 20 kV as driving voltage and 275 nm as detection wavelength. Repeatability tests showed that the R.S.D. of both intra- and inter-day migration times and peak areas were less than 5%. Recovery results ranged from 87.9% to 106.1%. Samples of A. margaritacea extracts were analyzed using the validated method, which is useful for its quality control.