SoxD subgroup genes, which belong to the Sox transcription factor family, have been implicated in the developing nervous system. Their expression has been seen in neural stem cells as well as differentiating neurons. However, despite their importance in development, a relatively low number have been characterized for freshwater fish. In this study, we were able to gain three full-length SoxD sequences from transcriptome sequencing data of carp: CcSox5, CcSox6 and CcSox13 (Cyprinus carpio SoxD).These genes were verified by sequencing, blast and homology alignment. CcSoxD have two to four exons and encode a 780, 784 and 602 amino acid protein, respectively. Chromosome synteny analyses revealed that CcSox5 and CcSox13 weretightly linked with the etnk gene, which was conserved in all species; however, there were no conserved regions flanking CcSox6. Numerous essential transcription factor binding sites (TFs) were predicted within the 2000 bp upstream of the 5’ end of these genes. These TFs include BSX, BRN4 and NGN–NEUROD, which have been shown to be involved in the early stages of neuronal determination and neurogenesis in vertebrates. Tissue distribution analyses by Quantitative real-time RT-PCR (qRT-PCR) revealed that CcSoxD genes were abundant in the brain, showed sexual dimorphism, and were inconsistently expressed during embryogenesis. These results indicated that CcSoxD plays an important role in the development of the nervous system and may be involved in sexual development in carp. And they provide a foundation for further study of the function of CcSoxD genes during carp development and neurogenesis.