The major histocompatibility complex ( MHC) of fish was used to study the genet ic structure as a molecular genetic marker of four populations of red common carp. Based on reported common carp MHC class .. gene sequences, a pair of specific primers was designed, MHC class .. molecular ..2 gene fragments were amplified from Xingguo red common carp ( Cyprinus carpio var. singguonensis ) , purse red common carp ( C. carpio var. wuyuanensis ) , glass red common carp ( C. carpio var. wananensis) , and Oujiang color common carp ( C. carpio var. color ) , then cloned and sequenced. The polymorphism of encoded MHC class ..molecular ..2 chain gene was rich, with 106 variable loci in 234bp in length. The percentage of polymorphism was 45. 3%, among the four populations, purse red common carp was significantly dif ferent from the other red common carps. The phylogenet ic trees constructed by encoded MHC class ..molecular ..2 chain gene and its amino acid sequences indicated identically, and the relationship between Xingguo red common carp and Oujiang color common carp was clo ser, belonging to one evo lutionary branch, whereas glass red common carp and purse red common carp belonged to the other two different evolutionary branches respectively. The purse red common carp is a more specialized group. The rich polymorphism of encoded MHC class .. molecular ..2 chain gene is suitable as a molecular genetic marker for different populations of common carp.