Melanocortin receptor 1 gene (mc1r) is a crucial regulatory factor for body color formation in animals. In order to explore the role of mc1r gene during body color variation in Amphilophus citrinellus, mc1r full-length cDNA was obtained for the first time by rapid-amplification of cDNA ends (RACE) technique. The total length of mc1r was 1 699 bp containing 497 bp 5′ untranslated region (UTR), 224 bp 3′-UTR, and 978 bp open reading frame (ORF) encoding 325 amino acids (Fig. 1). Sequence analysis of amino acids and phylogenetic analysis indicated that the similarity of mc1r encoded protein sequence of A. citrinellus showed 55.1%, 77.1%, 90.15% and 96.92% similarity with that of Homo sapiens, Danion rerio, Larimichthys crocea and Oreochromis niloticus, respectively (Fig. 4). Analysis revealed that mc1r was expressed at different levels in all 9 embryonic periods. With the development of embryo, the expression level of mc1r decreased gradually (Fig. 7). The results suggested that the basic expression level of mc1r initiated adenylate cycle in early stage of embryonic development, then involved in the formation of pigment cells. In three periods of body color changes (black to hoar to yellow), the expression of mc1r was decreased first and then increased slightly in caudal fin, scales and skin and its expression was the lowest in the gray white transition stage (Fig. 8). It was presumed that there might be a competitive combination between mc1r and Agouti, and that the color might be related to appropriate balance among three genes, mc1r, tyr, and tyr1 in the process of body color changes of A. citrinellus. When the fish grew to near maturity, individuals with incomplete black-fading showed higher mc1r expression compared to those with complete black-fading (P < 0.05, Fig. 9), and surface melatonin was negatively correlated with the mc1r expression. mc1r gene was expressed in all 11 tissues, and its expression in scale was significantly higher than in other tissues (P < 0.05, Fig. 10). The present study revelaed expression features of genes related to color variation, and the data are important for further studying fish body color heredity and body color improvement.