The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important freshwater aquaculture reptiles in East and Southeast Asia. In contrast to the other strains of this species, the Qingxi black turtle has black skin. In this study, three Qingxi black turtles (WBF) and three Dongting Lake turtles (DTF) were investigated to compare and analyze their differences in skin color by mRNA sequencing and miRNA sequencing. Total of 1,772 differentially expressed mRNAs were identified including 1,079 upregulated and 693 downregulated in WBF. Through miRNA sequencing, 1,071 miRNAs were identified. Three- hundred nineteen miRNAs were differentially expressed, including 187 upregulated and 132 downregulated, which corresponded to 38,563 target mRNAs. Nine differentially expressed mRNAs and twelve differentially expressed miRNAs were validated by qRT-PCR. Integrated analysis of the profiles of differentially expressed miRNAs and mRNAs predicted 2,262 miRNA-mRNA interaction sites. Several mRNAs (such as tyr, mitf, gpnmb and kit) and miRNAs (such as miR-138, miR-383-3p, miR-1388b-5p and miR-18a-3p-3) involved in turtle skin pigmentation were identified. The results obtained in this study concerning mRNA-miRNA regulatory networks may help to establish a foundation for future research on the mechanisms underlying pigmentation in P. sinensis.