Technical Abstract: Analytical methods for selenium (Se) speciation were developed using high performance liquid chromatography (HPLC) coupled to either inductively coupled plasma mass spectrometry (ICP-MS) or electrospray ionization tandem mass spectrometry (ESI-MS/MS). Separations of selenomethionine (Se-Met) and selenocysteine (Se-(Cys)2) with favorable peak shape and resolution were obtained by both HPLC-ICP-MS and HPLC-ESI-MS/MS. Both methods achieved low limits of detection, high sensitivity and favorable stability. With HPLC-ESI-MS/MS, signal suppression was observed when complex matrix was co-eluted, but excellent structural characterization was still achieved. Thus, HPLC-ICP-MS is better for the detection of Se species, and HPLC-ESI-MS/MS is essential for molecular identification and confirmation. A purified selenoprotein from M. anguillicaudatus muscle tissue was analyzed by the two complementary systems (HPLC-ICP-MS and HPLC-ESI-MS/MS) with high sensitivity and accuracy. The results demonstrated that Se-Met was the predominant selenoamino acid in the purified selenoprotein from M. anguillicaudatus muscle tissue, and the concentration of Se-Met was 6.280 mg/kg (dry mass). In addition, in HPLC-ICP-MS, an unknown Se-containing compound with similar polarity to Se-(Cys)2 was discovered. Using complementary data from HPLC-ESI-MS/MS, it was determined that this unknown Se-containing compound was not Se-(Cys)2.