We analyzed a litchi cultivar that included three phenotypes for pericarp color, ranging from green, indicating the absence of anthocyanins, to yellow, and red. Anthocyanins, chlorophylls, carotenoids, and flavonoids were measured in the three stages. Fruit coloration of red-skinned litchi was mainly due to higher flavonols, and anthocyanin pigments, lower chlorophyll (higher chlorophyll degradation). Expression of four genes of the anthocyanin pathway coding for phenylalanine ammonialyase, chalcone synthase, flavanone-3-hydroxylase, and the UDP-glucose: flavonoid-3-O-glucosyltransferase (UFGT), was analyzed by RT-PCR at three developmental stages from before the onset of ripening to full maturity. Gene expression patterns were compared to anthocyanin metabolites. The contents of anthocyanins and flavonols in the pericarps were consistent with the higher mRNA levels of UFGT, while, transcription of the other gene was not expected to follow the anthocyanin content. We suggest that UFGT might play an important role in anthocyanin biosynthesis in the pericarp of litchi. Thus, UFGT expression strongly influences fruit coloration in litchi.