Carotenoid mutants are useful for elucidating carotenoid metabolism. ‘Kusaie’ is a yellow-fruited form of ‘Rangpur’ (Citrus limonia Osbeck). Hyuganatsu (C. tamurana hort. ex Tanaka) is a medium-sized, light yellow fruit. Its bud mutation, wherein the fruit rind color becomes orange, is named ‘Orange-hyuga.’ To elucidate the mechanism underlying this alteration, their carotenoid composition and abscisic acid content were analyzed. In the flavedo of ‘Kusaie,’ significant phytoene accumulation, decreased xanthophyll, and ABA contents were observed, suggesting that phytoene desaturase was suppressed. Moreover, the total carotenoids in the juice sac of ‘Kusaie’ was significantly lesser than those in that of ‘Rangpur,’ suggesting that the production of carotenoids is suppressed in ‘Kusaie.’ In ‘Orange-hyuga,’ the total carotenoids was approximately 6-fold that of Hyuganatsu, and a significant xanthophyll accumulation, especially violaxanthin, was observed. Furthermore, ABA content was significantly lower. Accordingly, those might be associated with an altered gene expression balance upstream and downstream of biosynthesis. Difference in biosynthesis regulation in these color-altered cultivars might cause a change in the carotenoid contents and composition in fruits, which seemed to result in color changes from reddish-orange in ‘Rangpur’ to yellow in ‘Kusaie’ and from a light yellow color in Hyuganatsu to an orange color in ‘Orange-hyuga.’ In this study, these color-changing citrus mutants were observed to accumulate carotenoids differently from the original type, and we speculated that different changes occurred in carotenoid biosynthesis regulation.