Yellow mutant rainbow trout (YR) is becoming more popular for aquaculture production in China in recent years owing to its excellent meat quality and gorgeous appearance. Although much comparative research has been undertaken on two or three different skin colors of the same species, seldom attentions were focused on the genetic regulation during the developmental process of pigmentation. In this study, the skin transcriptomes in three distinct developmental stages of YR were sequenced to search for genes related to skin pigmentation. Overall design: In the present study, RNA-seq was used to identify the candidate genes that are responsible for color formation among three developmental stages of YR.