Melanocortin 1 receptor gene (mc1r) is an important gene that controls pigment synthesis in animals. To explore the relationship between mc1r gene expression level and body color variation in Rainbow Trout (Oncorhynchus mykiss), the present work obtained the full-length cDNA sequence of the gene by rapid-amplification of cDNA ends (RACE) technology, and the encoded protein was analyzed by bioinformatics. Simultaneously, quantitative real-time PCR (qRT-PCR) was used to detect the expression levels of mc1r gene in different developmental stages (from fertilization stage to 12 months post hatch) and tissues (dorsal skin, ventral skin, dorsal muscle, ventral muscle, eye, brain, gill, midkidney, headkidney, intestine, liver, spleen and heart) of wild-type and yellow mutant Rainbow Trouts, respectively. The results showed that mc1r gene was 4 518 bp, containing 1 017 bp open reading frame (ORF) (encoding 338 amino acid residues), 532 bp 5? untranslated region (UTR), and 2 969 bp 3? UTR. Sequence analysis revealed that Mc1r protein of Rainbow Trout had the 7TM_GPCR_Srsx structural domain, and sequence analysis of amino acids and phylogenetic tree analysis indicated that conservation of Mc1r was higher in fish than that in other vertebrates (Table 2 and Fig. 2). qRT-PCR results showed that mc1r gene began to express at the fertilized egg stage of wild-type and yellow mutant Rainbow Trouts, and the expression in the early embryonic stages (from fertilized egg stage to multi-cell stage) was higher than that in the late embryonic stages (Fig. 3). Moreover, there were significant differences (P < 0.05) in the expression level of mc1r gene at the same stages between wild-type and yellow mutant Rainbow Trouts, including fertilized egg stage, 4-cell, 16-cell, blastula, gastrula, neurula, somite stage, 1 day post hatch, 3 days post hatch, 7 days post hatch, 1 month post hatch, 2 months post hatch, 3 months post hatch and 6 months post hatch (Fig. 3). mc1r gene also widely expressed in various tissues in 12 months post hatch wild-type and yellow mutant Rainbow Trouts, with the higher expression levels in dorsal skin, ventral skin and brain, when compared to other tissues (P < 0.05) (Fig. 4). Moreover, the expression level of mc1r gene in dorsal skin of wild-type was higher than that of yellow mutant Rainbow Trout (P > 0.05) (Fig. 4). In conclusion, the expression level of mc1r gene might be closely related to body color variation of Rainbow Trout. The results of this study provided valuable data for later studies on the molecular mechanism of Rainbow Trout body color variation.