This study was conducted to analyze the coat color characteristics in Jeju Black Cattle by comparative the coat color patterns. Black and others coat color skin tissues were collected from 6 Jeju Black Cattle. RNA-seq analysis was conducted to identify coat color related genes and expression levels of the genes were identified using qPCR. Three different staining methods were used to examine the distribution of melanin in skin tissues. Results of RNA-seq analysis between black and others coat color skin tissues in Jeju Black Cattle. We found a total of 271 DEGs, with 42 genes up-regulated and 229 genes down-regulated. Hierarchical clustering analysis showed that the expression patterns of DEGs were different between black group and others color group. We conducted GO Term analysis and KEGG pathway analysis on the found genes to select candidate genes associated with coat color expression. Expression levels were identified using the qPCR for 8 (DCT, KIT, MC1R, OCA2, PAX3, PMEL, SLC45A2 and TRPV2) of the selected candidate genes. The expression level of the candidate genes in others coat color skin were identified to be at least 10 times to 33 times lower than that of the black coat color skin. Expression of genes identified by experiments showed the same expression pattern as that of bioinformatics analysis. Tissue staining was also conducted to determine the distribution of melanin and the like in the black and others skin. In the analysis, melanin component was identified in the black coat color skin. In this study, the difference of gene expression was identified by comparison between black skin and other skin in Jeju Black Cattle, and higher expressions were observed in black skin. The black and others skin transcript profile will help further research to understand gene expression networks that regulate skin physiology and melanogenesis in cattle.