The homology cloning and RACE PCR were employed to clone the MHC-Ⅱ β gene from cobia (Rachycentron canadium). The full length cDNA of MHC-Ⅱβ comprises 1 161 bp with a 20 bp 5′ untranslated region (UTR),a 394 bp 3′ UTR and a 747 bp open reading frame (ORF) encoding a polypeptide of 248 amino acid residues with a predicted molecular weight of 27. 99 ku and theoretical isoelectric point of 6. 21. The putative protein showed homology varying from 28. 5% to 77. 5% when compared with other fishes,mouse(Mus musculus),chicken(Gallus gallus)and human (Homo sapiens). The protein sequence showed all the important features including leader peptide,β1,β2,CP /TM /CYT regions and conserved cysteines. The MHC-Ⅱ β expression was detected in all tested tissues with different expression levels. The high expression was detected in head kidney,moderate expression was detected in gill,spleen and intestine,while low expression was detected in heart,brain and muscle.