Morphological characteristics of Changyong population of Chinese soft-shelled turtle(Pelodiscus sinensis) (Changyong turtle) native to Changyong Village, Hengyang County, Hunan Province were investigated by measuring body weight, body length, body height, carapace length, carapace width, plastron length, plastron width and calipash width. Changyong turtle and Dongting turle were cultured under the same circumstance to investigate breeding performance of these turtles aged 11-15 months, Quantitative RT-PCR was used to investigate the difference between Changyong turtle and Dongting turtle in relative expression of melanin genes, and spots counts were recorded to analyze spot characteristics. Phylogenetic tree was constructed to analyze genetic relationship of Changyong turtles based on mitochondrial Cytb, COI and 12S rRNA sequences. Genetic diversity of Changyong turtle was analyzed based on haploid diversity and nucleotide diversity. The results showed that 1) The length of the abdominal shell/back shell and the width of the abdominal shell/back shell of the Changyong turtle were 0.97±0.02 and 1.01±0.03, respectively, which was significantly smaller than those of the Dongting turtle, indicating back shell of Changyong turtle was smaller compared to Dongting turtle. 2) The highest values of absolute weight gain rate and instantaneous weight gain rate of Changyong turtle were 1.01 and 2.39, respectively, which was higher than those of Dongting turtle; the survival rate of Changyong turtle is 76.03, which is higher than that of Dongting turtle. 3) Changyong turtle has block shaped flower spots on its back, and the number and area of flower spots increase with body size during a certain period of time. After 14 months of age, the number of flower spots tends to stabilize. 4) The qPCR results showed that the relative expression levels of Tyr, Tyrp1, and Gpnmb genes in Changyong turtle were significantly higher than those in Dongting turtle(P<0.05), while the relative expression level of Ddc gene was significantly lower than that in Dongting turtle(P<0.05). there was no significant difference in relative expression level of Gch1 gene. 5) The haplotype diversity values of mitochondrial Cytb and COI in Changyong turtle are 0.817±0.055 and 0.906 ± 0.040, respectively, and the nucleotide diversity values are 0.0099±0.0019 and 0.0059 ± 0.0021, respectively; both values are at a high level, indicating rich genetic diversity. 6) The haplotype phylogenetic tree constructed based on mitochondrial Cytb, COI, and 12S rRNA sequences showed that the genetic relationship between Changyong turtle and Black turtle, Dongting turtle, and Huangsha turtle was relatively close, with a node support rate of over 96%.