High-performance liquid chromatography, coupled with photodiode array detection, was used to analyze the carotenoid composition of peel and juice vesicle tissues of ordinary and lycopene-accumulating mutants (referred to as red mutants in this article) of orange, pummelo, and grapefruit. Thirty-six major carotenoids, including some cis-trans isomers, were separated on a C30 reversed phase column, and 23 of them were identified on the basis of retention times and spectral characteristics with authentic standards. Carotenoid profiles varied with tissue types, citrus species, and mutations. beta-Citraurin occurred in the peel of oranges but not in juice vesicles, whereas the reverse was found for violaxanthin, 9-cis-violaxanthin, and luteoxanthin. The diversity of carotenoids in peel and juice vesicle tissues and the fact that there was over 250 times higher content of total carotenoids in peels of Yuhuan pummelo than juice vesicles suggested that the biosynthesis of carotenoids in these two tissues was independent and exchange of carotenoids between the tissues was not likely. Lutein was observed in peels of pummelos and grapefruits and juice vesicles of ordinary pummelo but not in orange tissues. Accumulation of lycopene and beta-carotene was observed in red mutant citrus, except for the peel of Cara Cara red orange. Additionally, phytoene accumulated in all tissues except for the peel of Chuzhou Early Red pummelo. No obvious change in the total content of xanthophylls was observed in the Cara Cara red orange. Ordinary grapefruit (Marsh) tissues and pummelo (Yuhuan) juice vesicles were almost devoid of carotenoids, and in red mutants, the content of total carotenoids increased dramatically up to 790-fold. The different changes in carotenoid content and profiles in mutant(s) of different citrus species suggest that the underlying mechanisms for the mutations might be different.