Abstract: A pair of degenerate primers were used to amplify polymorphic segments of the second exon of MHC class Ⅱ B genes from the genomic DNA of Alligator sinensis.Sequences were obtained from cloning,single strand conformation polymorphism analysis and sequencing.By comparing with another eight species MHC sequences,differences from sequences and variable sites were confirmed.Phylogenetic relationships were constructed by neighbor-joining method in MEGA and maximum parsimony method in PAUP4.0.Ten different nucleotide sequences were obtained，which were 166 bp long (except one 160 bp).There are 38 variable sites among ten nucleotide sequences and 23 variable sites among amino acid sequences.The number of nonsynonymous (dN) substitutions of pABS was higher than that of synonymous (dS) substitutions.The ten nucleotide sequences can be clustered into two clades (group A and B) in NJ and MP phylogenetic trees.Some specific sites were found between the two groups，including 9 nucleotide sites and 7 amino acid sites.The high polymorphism of MHC class Ⅱ B genes in A.sinensis was of great benefit to genetic conservation in the captive population of A.sinensis.