A novel method based on sweeping under pseudo stationary state and micellar electrokinetic chromatography(MEKC) was developed for the determination of shellfish toxins in shellfish samples.The capillary was firstly pre filled with the running buffer containing sodium dodecyl sulfate(SDS).By adjusting pH value，the electrophoretic flow of SDS micelle was equal to the counter electroosmotic flow(EOF).The positive charged shellfish toxins were injected electrokinetically into capillary,swept and adsorbed with SDS micelle.The injection time was prolonged to 320 s under 10 kV since the SDS micelles were at a pseudo stationary state.With the sweeping under pseudo stationary state method，the preconcentration factors of 950 and 810 were obtained for saxitoxin and domoic acid，respectively，compared with the traditionally electrokinetic injection MEKC.The method was used to the quantitative determination of saxitoxin and domoic acid with their detection limits of 0.05 ng/mL and 0.12 ng/mL，respectively.The proposed sweeping under pseudo stationary state and MEKC method was successfully applied in the determination of two shellfish toxins in shellfish samples.