Objective A method was developed for the determination of 4 selenium species including selenite [Se(IV)], selenate [Se(VI)], selenocystine (SeCys₂) and selenomethionine (SeMet) in Se-enriched functional food by anion exchange liquid chromatography-hydride generation-atomic flourence spectrometry. Methods Optimisation of the chromatographic conditions led to baseline separation of the four species in 12 min was achieved on a Hamilton PRP-X100 column (250 mm×4.1 mm, 10 μm) using elution with (NH₄)₂HPO₄ 40 mmol/L at pH=6.0 as mobile phase. Results The detection limits of Se(IV)、Se(VI)、SeCys₂ and SeMet were 0.85,1.07,0.91 and 1.73 μg/L. The correlation coefficients were above 0.999 5. The recoveries were in the range of 80.2%-108.7% for all the determinations, with the RSD less than 5.0%. 0.6 mol/L hydrochloric acid was suitable for inorganic selenium with extraction efficiencies above 92%. Organic selenium required an enzymatic reaction using protease K to give satisfactory extraction efficiency above 82%. Conclusion A rapid, simple and accurate method had been developed for the determination of selenium species, and the proposed method was applied to provide technical support for monitoring the selenium species in Se-enriched food supplements.