Chilin fish (Varicorhinus macrolepis) is classified as a second-class protected animal in China. The wild-type body color is predominantly black. however, recent observations have documented individuals with a gold color mutation. To identify the genetic mutations responsible for this change, we investigated the mechanisms underlying body color mutations in Chilin fish. Transcriptome sequencing was conducted on skin samples from wild-type and mutant fish. A total of 72,663 gene sequences were screened using the DESeq2 criterion (P-value < 0.05 and |log2 fold-change| > 1), identifying 605 up-regulated and 602 down-regulated genes in the mutant samples. A heatmap illustrated the expression differences between genes. Seven genes with significant differential expression were identified: LOC107600971, MLLT1, tmem41ab, LN590753, Zbed4, RASSF2, and LN590710. KEGG pathway enrichment analysis revealed their involvement in the p38 MAP kinase and nuclear factor NF-kappa-β p105 subunit signaling pathways. Transcriptomic data from wild-type and mutant skin tissues were provided, identifying seven DEGs associated with body color variation. Experimental analysis confirmed their strong correlation with body color mutation. We hypothesized that these two signaling pathways influence the body color mutation in Chilin fish. This finding enhances our understanding of the complex molecular mechanisms regulating body color mutations. Furthermore, it provides novel insights for investigating body color mutations in other Cyprinidae species.