Abstract: To study the structure and function of MHC (major histocompatibility complex) in Trachinotus ovatus, we obtained the full-length cDNA of ToMHCⅡβMHCⅡβ (major histoeompatibility complexⅡβ) gene from T.ovatus by RACE-PCR (rapid amplification of cDNA ends polymerase chain reaction) technology. This sequence was 1 472 bp, including an ORF (open reading frame) region of 747 bp. The peptide encoded MHCⅡβ gene could be divided into five parts, including signal peptide, peptide binding region, IGc1 domain, transmembrane region and cytoplasm area. A neighbor-joining tree shows that the MHCⅡβ gene from T.ovatus clustered into one cluster independently. It had close genetic-relationship with other fishes and farther genetic-relationship with amphibians and mammals. Homology analysis reveals that the ToMHCⅡβ shared 79% identity with Micropterus salmoides. In all 13 tissues, the highest expression level of MHCⅡβ gene was observered in spleen and kidne, while the minimum level existed in fin using qRT-PCR. Meanwhile,  MHCⅡβ gene mRNA expression levels were significantly up-regulated in intestine (at 3^rd hour), liver (at 12^th hour), spleen and kideny (at 24^th hour) after being infected with Photobacterium damselae, which indicates that this gene has important effects on immune response.