Abstract: Polymorphism of the second exon about SLA-DQB genes in some Chinese native pigs was investigated employing PCR–SSCP analysis and DNA cloning sequencing. Combined with the sequences in GenBank, 73 new alleles were gained, among them function alleles of SLA-DQB were sixty-eight, five alleles of pseudogene (SLA-DXB) were gained. There were disequilibrium distribution of the alleles in all breeds, the same allele was shared by most breeds. C08 allele existed in 11 breeds of six groups and in the wild pigs of Yunnan and Sichuan province, and its frequency reached 55.10%. More than five sequences were found in each individual, suggesting duplication in these loci examined, there were three copies about SLA-DQB genes. The variable sites based on nucleotide and amino acids reached to eighty-one and forty-nine, respectively. The values of allelic diversity (H=0.889) and the nucleotide diversity (Pi=0.047) were revealed very high, from both values of H and Pi were higher in the β pleated sheet region than those in α helix region in Chinese native pigs. In general, values of H and Pi in Huanan pigs and Xinan pigs were higher, vice versa in Tibet pigs. The genetic distance within group were showed the same order as comparison Pi values, hence we concluded the different rate of nucleotide substitution were positive correlated with the degree of nucleotide diversity in Chinese domestic groups. The genetic distances about SLA-DQB gene between groups were detected as follow: the great genetic distance were existed between the Jianghai and Huabei groups, and the smallest genetic distance were existed between the Huazhong and Gaoyuan groups.