Sox genes encode a family of transcription factors which are characterized by the conserved HMG domain and are involved in a diverse range of developmental processes. Using degenerate primer PCR, 7 different sequences encoding the HMG domains of Sox1, Sox9 and Sox1 1b were cloned and sequenced from genomic DNA in the red crucian carp (Carassius carassius red variety). In the case of Sox1 and Sox1 1b, we found evidence of gene duplication. In the phylogenetic tree, two paralogs of Sox1 1b (Sox1 1b1 and Sox1 1b2) fit within the clade of Sox11, especially in the Sox 1b subfamily, not in the Sox1 1a subfamily. Three Sox1 sequences (Soxl-1, Soxl-2 and Sox1-3) which shared the same amino acid sequence were identified in the red crucian carp. At the nucleotide level, Soxl-1 shared the highest sequence similarity to the zebrafish Sox1a, and Sox1-2 and Sox1-3 showed the highest similarity to the zebrafish Sox1b. The phylogenetic tree clearly demonstrated that the red crucian carp Sox1-1 clustered together with the zebrafish Sox1a, and the red crucian carp Sox1-2 and Sox1-3 with the zebrafish Sox1b. The result suggested that the red crucian carp Sox1-1, Soxl-2 and Sox1-3 were resulted from duplication of Sox1 gene rather than polymorphisms of the same gene.