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Sox gene is a large gene family which encodes transcription factors and contains a HMG box that is responsible for a variety of developmental processes. In the present study, we obtained fifteen clones representing Sox gene HMG-boxes from male and female Hyla sanchiangensis, distributed as Sox1, Sox2, Sox3, Sox4, Sox11, and Sox33. The sequences analysis indicated that Sox1 and Sox4 have two duplicated copies, respectively, Sox2 has three duplications and Sox11 has six different copies. Furthermore, the amino acid of Sox1, Sox2, Sox4 and Sox11 duplicated copies has been exchanged indicating that the gene functional selection might be necessary for Sox gene duplicated process. Phylogenetic analysis was carried out and suggested that HMG domain-encoding sequences are members of the SoxB and SoxC groups. The topologies implied that the duplicated Sox genes might evolve independently in H. sanchiangensis. Substitution rate showed that the evolutionary behaviors of Sox duplicated copies are dissymmetry, which would cause two parallel evolutionary patterns at the molecular level. One is the duplicated genes were suffering from a period of relaxed selection and caused the asymmetric evolutionary rate in one copy, then accelerated gene evolution. Another is that the Sox duplicated genes experienced identical selection constraints and had no greater genetic diversity. In this case, we proposed that all Sox genes in H. sanchiangensis obtained in this examination are under strong purifying selection, and duplicated Sox genes evolved independently.