Sox genes of vertebrate are highly evolutionarily conserved, which encode different transcriptional factors involved in various developmental processes. Sox family is characterized by a sequence-specific DNA binding HMG-box containing about 79 amino acids. To realize the complexity of genes of the Sox family in the structures, functions and their evolutionary relationships, in the present study by utilizing all available complete nucleotide/protein sequence data of vertebrate Sox genes, we performed multi-sequence comparison and construction of phylogenic tree, and the grouping of Sox family members and the pattern of their molecular evolution was also analyzed.