Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract colouration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana ‘Mrs. Butt’, a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5 Gb with a scaffold N50 of 151,756,278 bp and contains 86,572 genes which undergone a recent WGD. We confirmed that multiple rounds of whole genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colours in Bougainvillea, we analyzed the genes involved in betalains and anthocyanins biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with the bract colour, and the higher expression level in the betalain biosynthetic pathway is required for the coloured bract. The improved understanding of the correlation between gene expression and bract colour allows plant breeding outcomes to be predicted with greater certainty.