The mandarin fish, Siniperca chuatsi is an important species in the aquaculture industry of China. The understanding of its immune system is essential for such aquacultural purpose. On the basis of the serum immunoglobulin (IgM) purification from the fish, the present study aims to clone the cDNAs encoding the heavy (IgH) and light (IgL) chains of the IgM, and then express them respectively in Escherichia coli. The serum IgM from S. chuatsi was purified for the first time in China by using affinity chromatography techniques, with the molecular weight of the IgH and IgL being determined to the 72kD and 29kD, respectively. The rabbit antisera which were developed against the purified IgM, reacted more strongly with the IgH than with the IgL chain, as revealed by the Western blotting analyses. The full-length cDNAs encoding the IgH and IgL chains of the mandarin fish were for the first time cloned by RT-PCR and RACE. The amino acid (aa) sequence of the IgH was compared with those of other teleost fish, and the phylogeny tree was constructed according to the aa sequences of IgM-CH4 domains from 18 vertebrates. The evolution of CH4 domains was then discussed, and the divergence time between S. chuatsi and the other species estimated. When the aa sequences were compared between the IgL chain of the mandarin fish and those of other actinopterygian fishes, it is found that the unique trinucleotide sequence repeat (AGC)n encoding serine in the CL domains exists in S. chuatsi and another perciform species. The phylogeny tree constructed by aa sequences of the CL domains from 20 vertebrates suggested that the IgL of the mandarin fish was similar to the G isotype of Channel catfish, Ictalurus punctatus and to the L1 isotype of rainbow trout, Oncorhynchus mykiss, but not to the κ or λ isotype of higher vertebrates. The recombinant expression plasmids carrying the cDNA sequences of mandarin fish IgH and IgL chains were then constructed respectively, and subsequently expressed efficiently in E. coli. Using Western blotting analyses, the products expressed by the inserted genes were recognized by the rabbit anti- purified-mandarin-fish-IgM sera, confirming that the cloned cDNAs do encode the mandarin fish IgH and IgL chains.