Abstract: The genetic diversities of nine Chinese indigenous chicken breeds were investigated by sequencing the MHC B-L exon 2. According to allele frequencies of MHC B-L exon 2， genetic parameter and Tajima-Nei genetic distances and Maximum Likelihood genetic distances were calculated for each breed. By the Neighbor-joining and FitchMargoliash methods， phylogenetic trees were obtained based on two types of genetic distances. The results showed gene flow was the major factor affecting genetic diversities of nine Chinese indigenous chicken breeds. The phylogenetic relationship among different chicken breeds population was in accordance with their localities and breeding history.

Key words: MHC, genetic marker, genetic parameter, phylogenetic tree