To learn how to regulate carotenoid content in citrus fruit, we studied the mechanism of carotenoid accumulation using physiological and genetic methods. Based on differences in the carotenoid profiles of flavedo and juice sacs, citrus species could be roughly divided into three groups: carotenoid-poor, violaxanthin-abundant, and β-cryptoxanthin-abundant groups. A comparison of the gene expression among several citrus species with different carotenoid profiles showed that the difference in carotenoid profiles among citrus species was highly regulated by coordination of the expression for genes related to carotenoid biosynthesis and catabolism. Quantitative trait loci related to carotenoid content were also identified to select progeny with high carotenoid content. Moreover, we showed that the effect of postharvest ethylene on carotenoid accumulation in flavedo varied with temperature. Under an ethylene atmosphere, in flavedo, carotenoid accumulation was enhanced more dramatically than under an ethylene-free atmosphere at 20°C but repressed at 5°C.