The cloning process of full-length cDNA of MHC class Iα gene from swamp eel (Monopterus albus) was reported in the paper. The full length of cDNA, encoded with 350 amino acids, was 1 731 bp, including a 5 untranslated region (UTR) with 78 bp-long, and 3′ UTR with a 600 bp-long. The genomic sequence was identified to be different from that of in other teleosts, which contained of four exons and three introns. Real-time quantitative PCR demonstrated that the MHC class Iα gene ubiquitously expressed in ten healthy tissues. Great changes in liver, spleen and kidney were observed after they infected by Aeromonas hydrophilia, a pathogenic bacteria. Fifty distinct alleles were isolated from forty-two individuals, and each of them had one to six alleles. The presence of six alleles in one individual suggested that there were at least three MHC Iα loci in the genome. Both at the protein-binding region (PBR) and at the non-PBR region, dN were significantly greater than dS (P<0.05), which implied that the gene undergone a strong positive selection in swamp eel sequences.