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Citrus fruits are an important nutritional source for human health and have immense economic value. Fruit development and ripening are key processes in the production of the phytonutrients, which are essential for a balanced diet and for disease prevention. The anthocyanins are responsible for red pigmentation in the flesh of sweet orange and one of the most important antioxidant compounds together with carotenoids (in particular lycopene) and ascorbic acid. These compounds contribute to protect against certain cancers, cardiovascular diseases, and other degenerative processes. The anthocyanin pathway is well described, and gene coding enzymes of the biosynthesis sequenced and analyzed at the molecular level. The generally identical structure and composition of genes taking part to anthocyanins pathway and their higher expression in blood oranges compared to common ones, suggested the investigation on regulatory network, in particular MYB transcription factors that play an important role in activation of the biosynthesis. In a recent study, the association of a long terminal repeat (LTR) to a Myb-like gene was found correlated to the red pigmentation in the flesh fruits of sweet orange cultivars. Citrus fruits are important also for their content of ascorbic acid. The gene transcription of key enzymes involved in the four known biosynthesis pathways of the vitamin C resulted up-regulated specifically in fruit, contributing to the high vitamin C accumulation in juice sacs. Moreover, new data related to the GalUR gene family in the citrus genome may suggest its involvement. The expected variability within Citrus species is low, due to the origin by spontaneous mutation and vegetative propagation, leading to a narrow genetic basis. Sweet orange, lemon, lime and grapefruit, are characterized by high heterozygosis, but nearly all cultivars are similar, as they originate from a common ancestor hybrid. Single nucleotide polymorphisms (SNPs) identification performed on vari