Abstract: 220 bp fragments of Sox gene HMG-box in Alligator sinensis were amplified by PCR,and then subcloned and sequenced.Four different Sox genes were thus identified in both male and female.The encoded amino acid sequences exhibited 91%,96%,100%,and 96% of sequence homology with those reported for human SOX gene HMG-boxes,respectively.According to nomination system of human SOX genes,the newly identified Alligator sinensis Sox genes were named as ASSox1,ASSox2,ASSox11,ASSox22,respectively.There was no sexual difference in the four fragments.The amino acid sequences coded by Sox genes from amphibian,reptile,bird,and human showed a high degree of sequence homology within the respective four clusters,as revealed in phylogenetic tree constructed.The results indicated that Sox genes were highly conservative in phylogeney.