Selenium-dependent glutathione peroxidase(denoted as Se-GPx)plays an important role in the enzymatic antioxidant defense system. It clears the reactive oxygen species (ROS) to avoid the cellular damage. In order to study the function of Se-GPx in immune system and the ovarian development of Penaeus monodon, the full-length cDNA sequence of Se-GPx from black tiger shrimps (denoted as Pm Se-GPx) was obtained by high-throughput transcriptome sequencing and RACE. The full-length cDNA of Pm Se-GPx is 959 bp, including an open reading frame (ORF) of 639 bp encoding a polypeptide of 212 amino acids, a 5'UTR of 10 bp and a 3'UTR of 310 bp containing a conserved selenocysteine insertion sequence (SECIS) element. The molecular mass of the deduced amino acid (aa) sequence was 23.65 kDa with an estimated pI of 4.61. Blast and phylogenetic analyses suggest that Pm Se-GPx is a new member of the shrimp GPxs family. The tertiary structure of Pm Se-GPx protein presents like a bag and there is a catalysis site, which contains couplet of four conservative residues (cysteine C/selenocysteine U, glutamine Q, tryptophan W and asparagine N). Pm Se-GPx mRNA expression was detected in nine tissues by real-time PCR. Pm Se-GPx mRNA expressed was the highest in the hepatopancreas and moderate in the ovary. The result showed that Pm Se-GPx was expression mainly in hepatopancreas which plays an important role in detoxification. At different stages of ovary development, Pm Se-GPx was expressed highly at StageⅢ and Stage V, which indicated a large number of ROS may be produced during these development stages. Pm Se-GPx may protect the ovary from the oxidization damage. Under the stress of Cu²⁺, the expression of Pm Se-GPx showed a trend of decline, but recovered at 48 h, and then decreased. The result showed that the stress of Cu²⁺ may inhibit the expression of Pm Se-GPx. Under the stress of pH 9, expression trend of Pm Se-GPx first declined, but recovered at 24 h, then rose significantly at the 96 h. The result showed that neutral environment may inhibit the expression of Pm Se-GPx but aqueous alkaline medium may promote it. Presumably, Se-GPx plays an important role during the ovarian development and immune regulation of P. monodon. Our study provides a basis for further research in reproduction and immunology of P. monodon.