To gain a comprehensive and unbiased molecular understanding in different skin color of P. leopardus, we uesd Illumina HiSeq 2500 and TMT to compare transcription and protein levels between red and black skin of P. leopardus. There were showed that the metabolic activity of pigment cells in red skin is more vigorous, more prone to migration, and the level of melanin synthesis is lower. These findings further enrich the current basic data on fish skin color research, especially fill in the information of protein level, which is of great significance for a deeper understanding of the skin color regulation mechanism of P. leopardus and even coral reef fish.