The major histocompatibility complex (MHC) class II A gene plays an important role in the immune response of teleost. In this study, the full length of MHC IIA cDNA and genomic sequences were obtained from healthy Oreochromis niloticus by homology cloning and rapid amplification of cDNA ends polymerase chain reaction (RACE-PCR). The full-length of cDNA sequence (Orni-DBA*0101, GenBank No: JF719813) comprises 1 205 bp with a 720 bp open reading frame (ORF) encoding a predicted protein with 239 amino acid residues. The genomic sequence was further identified to be 1 388 bp in length, which contains four exons and three introns. Eight class IIA alleles were identified from four healthy O. niloticus individuals. The variability that existed in the α-1 region was higher than that of half-smooth tongue sole. All the characteristic domains present in MHC IIA of other species could be found in O. niloticus MHC IIA sequence, including a leader peptide, two extracellular domains, a transmembrane region, and a cytoplasmic domain. In addition, there are four conserved cysteine residues and abundant phosphorylation sites. The deduced amino acid sequence shares 23%－65% identity with those of other vertebrates. Semi-quantitative reverse transcriptase PCR (RT-PCR) demonstrated that O. niloticus MHC IIA mRNA was ubiquitously expressed in all tested tissues, which is highly expressed in spleen, kidney, gills, liver, heart, gonad and gut, however, lowly expressed in muscle and bladder. Challenge of O. niloticus with pathogenic bacteria, Aeromonas hydrophila, results in a significant change of the expression of MHC IIA in the liver, spleen, kidney, gills and intestine. The result implied that MHC IIA might play an important role in the immune system.