The occurrence of betalains and anthocyanins is mutually exclusive, which is a curious phenomenon in the plant kingdom, and the biochemical mechanisms for this restriction are unknown. In the present study, we performed transcriptome analysis of two betalain-producing species, red Bougainvillea glabra Choisy. 'Sanderiana' (R) and white B. glabra 'Alba' (W) by transcriptome sequencing. In total, we obtained 69692 (Red) and 60727 (White) genes with an average length of 665 and 728bp respectively. Out of 3106 significantly differentially-expressed genes (71%), 1003 were R-specific (32%), and 1605 were W-specific (52%). To validate betalain-/anthocyanidin-biosynthesis genes detected (cytochrome P 450 76AD1 (CYP76AD1), dihydroxy-phenylalanine (DOPA)-4,5-dioxygenase (DODA), cyclo DOPA-5-O-glycosyltransferase (cyclo-DOPA-5-GT) dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX)), real-time PCR was performed in leaves and three development stages of flowers in four Bougainvilleas, red R, white W, orange Bougainvillea×buttiana 'Salmoea' (O) and purple B. glabra 'Formosa' (P). Contents of betalains were also measured. The results showed that betalains accumulation was consistent with the expression level of DODA in O. A correlation between expression of CYP76AD1 and cyclo-DOPA-5GT and betalains was not discovered. This suggests that production of betacyanins was under the regulation of more complex factors. Both DFR and LDOX responsible for anthocyanidin production were first validated in floral organs and leaves in betalain-producing plants by real-time PCR. These findings suggest a fully functioning anthocyanin pathway, at least, to the stage of LDOX in bougainvilleas.