Carotenoid pigments are responsible for many color hues in fishes. Fishes cannot synthesize carotenoids endogenously, but dietary carotenoids were derived from food. Carotenoid-based coloration is influenced by pigments in diet, chromatophore and the interaction of cells. Much less is known about the mechnisms of carotenoid-based coloration in fishes, particularly in the understanding of carotenoid metabolism pathways and the molecular basis of carotenoid coloration. In this paper, the correlations of genetic basis, physiological condition and environmental factors with carotenoid pigmentation in fishes were examined. Furthermore, molecular basis regarding the coloration process was reviewed. Gaps in our knowledge are discussed in the last part of this review. It is expected to provide some useful information for conducting similar research in China.