Selenium (Se) is an essential trace element in vivo involved in the defense against oxidative stress. Se deficiency is associated with many human diseases. The bioactivity of Se is dose-and species-dependent. Silkworm pupa has been reported to accumulate Se mainly in proteins. Thus the characterization of major Secontaining proteins is very important in the application of Se-rich silkworm pupas in food and drugs. In this study, crude proteins were extracted from Se-rich silkworm pupas, followed by DEAE-Sepharose and Sephedex G-75 chromatography. Se content was measured after each step to determine the highest Secontaining fraction for the next step of separation. The proteins obtained were analyzed using SDS-PAGE, followed by in-gel digestion with trypsin, and were characterized by MALDI-TOF MS and ESI-MS/MS. These data showed two proteins mainly accumulated Se in the silkworm pupas. Those two proteins were proven by mass spectrometry to be arylphorin and sex-specific storage-protein 2 precursor (SP-2), respectively. Both of them belong to the storage proteins of amino acids during metamorphosis and the non-feeding pupal stage. The results suggest that Se could be enriched by storage proteins and be supplied to silkworm pupas in accompany with amino acids for the synthesis of new Se-containing proteins and peptides.