Pelodiscus sinensis is rich in a variety of nutrients and possesses a broad range of edible and medicinal properties, consequently, this species has a long history of culture in China and other Asian countries. A strain of P. sinensis named the ‘Yongzhang golden turtle’ was created by selective breeding methods over a period of 16 years and was approved as a new strain by Chinese government. In contrast to P. sinensis with atrovirens coloration, which belongs to the Yellow River wild type strain, the body coloration of the Yongzhang golden turtle is yellow. The especial yellow coloration will possess a high ornamental value. However, the specific mechanisms underlying this coloration change have yet to be investigated. In our present research, we measured the calipash hue of the Yongzhang golden turtle and atrovirens wild type turtle using indices defined by the International Commission on Illumination lightness, red/green and yellow/blue (CIE-LAB), this analysis showed that the calipash hue of atrovirens wild type turtle was atrovirens, while, that of Yongzhang golden turtle was yellow. Compared with atrovirens wild type turtle, there was no obvious accumulation of melanin granules in the epidermis of the Yongzhang golden turtle, as determined by hematoxylin-eosin (HE) staining and transmission electron microscopy (TEM). We also determined that the levels of melanin (P < 0.01) and 5,6-dihydroxyindole-2-carboxylic acid (DHICA) (P < 0.05), which is melanin precursor, were significantly lower in the Yongzhang golden turtle than those in atrovirens wild type turtle. In addition, we cloned three key genes in the melanogenesis pathway, tyrosinase (tyr), tyrosinase-related protein 1 (tyrp1), and tyrosinase-related protein 2 (tyrp2 or dct), and compared these gene sequences between two strains of turtles. Analyses identified a single base mutation in tyrp1 within exon 8 that may be a cause for the yellow coloration of the Yongzhang golden turtle. Further analysis showed that the expression levels of these key genes in different tissues were all significantly down-regulated in the Yongzhang golden turtle, consistent with the reduced levels of DHICA and melanin. In summary, we preliminarily investigated the one of mechanisms underlying the novel body coloration of the Yongzhang golden turtle and provided guidance for further research.