Fruit coloration is one of the main quality parameters of Citrus fruit primarily determined by genetic factors. The fruit of ordinary sweet orange (Citrus sinensis) displays a pleasant orange tint due to the accumulation carotenoids, representing b,b-xanthophylls more than 80% of the total content. Pinalate is a spontaneous bud mutant derived from sweet orange Navelate, characterized by yellow fruits due to elevated proportions of upstream carotenes and reduced b,b-xanthophylls. To identify the molecular basis of Pinalate yellow fruit, a complete characterization of carotenoids profile together with transcriptional changes in carotenoid biosynthetic genes were performed in mutant and parental fruits during development and ripening. Pinalate fruit tissues showed a distinctive carotenoid profile at all ripening stages, accumulating phytoene, phytofluene and unusual proportions of 9,15,9´-tri-cis- and 9,9´-di-cis-z-carotene, while content of downstream carotenoids was significantly decreased. Transcript levels for most of the carotenoid biosynthetic genes showed no alterations in Pinalate; however, the steady-state level mRNA of z-carotene isomerase (Z-ISO), which catalyses the conversion of 9,15,9´-tri-cis- to 9,9´-di-cis-z-carotene, was significantly reduced in Pinalate fruit and leaf tissues. The isolation of the Pinalate Z-ISO genomic sequence identified a new allele with a single nucleotide insertion at the second exon, which generates an alternative splicing site that alters Z-ISO transcripts encoding non-functional enzyme. Moreover, functional assays of citrus Z-ISO in E.coli showed that light is able to enhance a non-enzymatic isomerization of tri-cis to di-cis-z-carotene which is in agreement with the partial rescue of mutant phenotype when Pinalate fruits are highly exposed to light during ripening. The defect in Pinalate Z-ISO gene causes a bottleneck in the carotenoid pathway with an unbalanced content of carotenes upstream to b,b-xanthophylls in fruit tissues. Taken together, our results indicate that a spontaneous single nucleotide insertion in Z-ISO is the molecular basis of the altered pigmentation in Pinalate sweet orange mutant and points this isomerase as an essential activity for carotenogenesis in citrus fruits.