A simple and inexpensive CE method was developed for the determination of peimine and peiminine. Because of the lack of an UV chromophore of peimine and peiminine, the detection method chosen was indirect UV detection, with N-(1-naphthyl)ethylenediamine dihydrochloride (NED) as the UV absorbing probe. It was thought that NED, a chromophoric ion, may form hydrogen bonding pairs with the analytes to cause significant changes in separation selectivity. Additionally, the hydrophobic interactions between analytes and the probe also play a crucial role in achieving a resolution between the two analytes. The analyses were carried out with a background electrolyte composed of 66% MeOHACN (1:1, v/v), 34% aqueous buffer containing 15 mM NaH2PO4, 2.5 mM NED, 4 mM H3PO4. MeOHACN mixtures used as organic modifiers can not only reduce the adsorption of NED to the capillary wall, but also decrease the baseline noise and drift. The method provided a linear response ranging from 5 to 200 mu g/mL. The limits of detection (LODs) for peimine and peiminine were 3.9 and 4.1 mu g/mL, respectively. The repeatabilities (n = 3) reached relative standard deviation values (RSDs) of 3.4 and 4.1% for the peak areas, 4.0 and 4.4% for the peak heights, and 0.29 and 0.30% for the migration time of peimine and peiminine, respectively. Regression equations revealed linear relationships (r = 0.99950.9996) between the peak area of each analyte and the concentration. The method developed was successfully applied to quantify peimine and peiminine in chloroform extracts of the ground Bulbus Fritillariae Thunbergii.