Abstract: Sinilabeo decorus tungting (Nichols) is a wild endemic fish in Hunan Province, however, due to overfishing and environmental damage, the germplasm resources of wild S. decorus tungting are scarce. In order to effectively protect germplasm resources of S. decorus tungting, artificial breeding research has been carried out. In the process of domestication and parental cultivation, it was found that there were two somatotypes in the wild population: the high-back type and the flatback type. The countable traits analysis showed that there was no significant difference between the two different somatotypes S. decorus tungting on fin formula and scales. To explore the genetic differences between the two somatotypes of S. decorus tungting, Cytb and ITS1 gene sequences were used as molecular markers to analyze the genetic differences. The results showed that based on the Cytb and ITS1 gene sequences, both the high-back type and the flatback type were showed a bias in base composition. And two somatotypes of S. decorus tungting were showed high haplotype diversity and low nucleotide diversity. In addition, the results of genetic distance analysis and NJ tree construction showed that the degree of genetic differentiation of the two somatotypes was low, which did not reach the level of population differentiation. In conclusion, the high-back type and flatback type belongs to the same population. The results of this study enriched the molecular biological data of S. decorus tungting, and provided theoretical basis for the protection and industrial development of S. decorus tungting germplasm resources. The reasons for the formation of the high back type of S. decorus Tungting was unknown and needs further study.