Carotenoids are the main pigments responsible of the colouration of Citrus fruits. The β-cyclization of lycopene, catalysed by the lycopene β-cyclases (β-LCY), seems to be a key regulatory step of the carotenoid pathway. In the present study, two β-LCYs from orange fruits (Citrus sinensis), named Csβ-LCY1 and Csβ-LCY2 have been isolated and the activity of the encoded proteins was demonstrated by functional analysis. Csβ-LCY1 was expressed at low levels and remained relatively constant during fruit ripening while Csβ-LCY2 showed a chromoplast-specific expression and a marked induction in both peel and pulp of orange fruits in parallel with the accumulation of β,β-xanthophylls. The potential involvement of Csβ-LCY2 in the accumulation of lycopene, characteristic of some Citrus species such as red grapefruits, was investigated. Expression of Csβ-LCY2 and another seven carotenoid biosynthetic genes were studied in the peel and pulp of the high lycopene-accumulating grapefruit, Star Ruby, and compared with those of ordinary Navel orange. In Star Ruby, the accumulation of lycopene during fruit maturation was associated with a substantial reduction in the expression of both β-LCY2 and β-CHX genes with respect to Navel orange. Moreover, two different alleles of β-LCY2: β-LCY2a and β-LCY2b were isolated from both genotypes, and functional assays demonstrated that the lycopene β-cyclase activity of the allele b was almost null. Interestingly, Star Ruby grapefruit predominantly expressed the unfunctional β-LCY2b allele during fruit ripening whereas Navel oranges preferably expressed the functional allele. It is suggested that the presence of diverse alleles of the β-LCY2 gene, encoding enzymes with altered activity, with different transcript accumulation may be an additional regulatory mechanism of carotenoid synthesis involved in the accumulation of lycopene in red grapefruits.