Abstract: In this study, a survey of the germplasm resources of Chinese soft-shelled turtle (Pelodiscus sinensis) was carried out in the drainage area of Dongting Lake and Yuanjiang River in Hunan Province. P. sinensis with nine pairs of ribs was found. In order to reveal its resource distribution, morphological characteristics and genetic characteristics, a comparative study of morphological markers, mitochondrial DNA, and polymorphisms of genes related to bone development was conducted in P. sinensis with nine pairs of ribs (R9) and P. sinensis with eight pairs of ribs (R8). As a result, a total of 331 R9 were obtained from 12222 cultured P. sinensis in Yuanjiang, Yiyang, Changde and Yueyang, accounting for 2.2%—3.1% of the total population. There are 11 thoracic vertebraes and nine pairs of ribs in the carapace of the R9, which is one thoracic vertebra and one pair of ribs more than the R8. Besides, the carapace width/carapace length, rear side skirt width/carapace length of the R9 were significantly smaller than those of the R8, and the body height/carapace length was significantly larger than that of the R8. Genes including CO I, Cytb, and 12S rRNA in the R9 and P. sinensis shared more than 99% homology. The phylogenetic analysis showed that the R9 and the P. sinensis clustered into one branch, there are shared haplotypes with the geographical populations of the Pelodiscus sinensis, and no population-specific markers were found. A total of 4 mutation sites were detected on the exons of RUNX2 and VRTN between R9 and R8, namely g.977380 C>T, g.6014427C>T, g.6015734A>C and g.6015864A>C. What’s more, there was a significant correlation between the g.6015864A>C mutation of VRTN gene and the number of thoracic vertebrae of P. sinensis (P<0.05). The above studies showed that R9 belongs to the P. sinensis, and its morphological structure differs from that of the R8 in which R9 has one more thoracic vertebra and one pair of ribs. The mutation site g.6015864A>C of VRTN gene may be related to the polyvertebrae trait of the P. sinensis. This study has important theoretical reference value for understanding the germplasm characteristics and seed industry innovation of P. sinensis.