A micellar electrokinetic capillary chromatography (MEKC) method for the separation and quantification of the coumarins in Cnidii Fructus was developed for the first time. Within 25 minutes, 5 major coumarins were separated using 18 mM borate, 12 mM phosphate and 50 mM SDS (pH 9.2) containing 20 % methanol. The relative standard deviations of migration times and peak areas were less than 5 %. The total contents of the five coumarins in plants from different habitats ranged from 13.6 to 44.6 mg/g, and recoveries ranged from 96.0 to 102.8 %. The effects of buffer concentration, SDS, pH value and organic modifier on the separation were investigated.