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To aid the breeding of citrus (Citrus sp.) for high carotenoid content, we assayed the fruit flesh of 48 cultivars and selections within a parental population consisting of both old and new cultivars and selections at two locations in Japan. The mean total carotenoid (CAR) content across all 48 cultivars and selections over the two locations was 26.59 μg·g−1 fresh weight (FW). The most prominent carotenoid was β-cryptoxanthin [BCR (12.09 μg·g−1 FW)] followed by violaxanthin [VIO (8.04 μg·g−1 FW)], ζ-carotene (2.27 μg·g−1 FW), phytoene (1.86 μg·g−1 FW), and β-carotene (0.96 μg·g−1 FW). Broad-sense heritabilities of CAR, BCR, and VIO were 0.80 or greater based on a sample of five fruit on one tree per location in one time sampling for 1 year in a location, which were revealed to be large enough for gauging the genetic variation. The mean CAR and BCR contents in a cultivar and selection group in advanced generations were nearly the same as in the initial population, suggesting no or little selection pressure on carotenoid content in the citrus breeding so far. High carotenoid contents in cultivars and selections released or selected recently, which have high fruit qualities, suggest their high potential for combining high fruit quality and high carotenoid content in breeding. We showed that the critical phenotypic value used in selecting hybrid seedlings can be determined from the estimate of environmental variance.