To quantify the 18 carotenoids on the basic routes of the carotenoid biosynthesis in plants simultaneously, a method for liquid chromatography-mass spectrometry (LC-MS) using atmospheric pressure chemical ionization was developed. With this method, the seasonal changes of carotenoids in the flavedo and juice sacs of 39 citrus varieties were analyzed. On the basis of the patterns of seasonal changes of carotenoids in both flavedo and juice sacs, 39 citrus varieties were classified. In flavedo, 39 varieties were classified into 5 clusters, in which the carotenoid profiles were carotenoid-poor, phytoene-abundant, violaxanthin-abundant, violaxanthin- and beta-cryptoxanthin-abundant, and phytoene-, violaxanthin-, and beta-cryptoxanthin-abundant, respectively. In juice sacs, they were classified into 4 clusters, in which the carotenoid profiles were carotenoid-poor, violaxanthin-abundant, violaxanthin- and phytoene-abundant, and violaxanthin-, phytoene-, and beta-cryptoxanthin-abundant, respectively. In flavedo, many citrus varieties, except for the carotenoid-poor and phytoene-abundant varieties, massively accumulated beta,epsilon-carotenoids (e.g., lutein), beta,beta-carotenoids (e.g., beta-cryptoxanthin and violaxanthin), and phytoene, in that order. In juice sacs, the accumulation order among beta,beta-carotenoids was observed. Violaxanthin accumulation preceded beta-cryptoxanthin accumulation in violaxanthin-, phytoene-, and beta-cryptoxanthin-abundant varieties. In each variety, the carotenoid profiles of the flavedo and juice sacs on the basis of the concentration in violaxanthin and beta-cryptoxanthin were similar, with the exception of a few varieties.