Abstract: Cognition of MHC (Major histocompatibility complex)has been developed from only as an explanation of the phenomenon related with histocompatibility and exclusion to a gene group referred to resistance and all immune response at present. MHC gene is the ancestral sequences that existed before separation of species, and has evolved and generated significant diversity among species and among individuals in the same specie. The difference of gene structure appears among different species in a present or absent gene framework, or a highly plastic region or a single cola or multiple coli in genome or in an arrange manner and the amount of coli and alleles. A similarity of gene structure exists among relative species, however, difference has been found in the types of genomic rearrangement and pseudogene. A highly polymorphic alleles exhibit among individuals in the same specie and its genetic basic is point mutation based on some nucleotide substitution. The factors in environment, such as pathogen-mediated selection pressure are most likely to drive this process. In some research, the MHC haplotype or the locusspecific cluster with resistance to specific pathogen has been detected. The peptide binding region (PBR) in MHC is among the most polymorphic regions found in vertebrate taxa, while the affinity between PBR and antigen peptide results in disease resistance or susceptibility for animals. New techniques of molecular biology and bioinformatics provide available tools to investigate MHC polymorphism, especially to explore the mechanism of mutual action between MHC molecule and epitope.