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Strelitzia reginae is a popular cut flower that has blue petals and orange sepals. Flower color is an important plant trait; however, little is known about its molecular mechanisms in S. reginae. In this study, cDNA libraries were constructed for blue petals and orange sepals of S. reginae. A total of 75 487 unigenes were obtained from transcriptome sequencing and de novo assembly, of which 41.86 % were annotated by public databases. Ultra-high performance liquid chromatography analysis revealed that anthocyanins were the main pigment in blue petals, and that carotenoids controled pigment formation in the orange sepals. Using a system analysis-based approach, 73 and 29 candidate genes related to anthocyanin and carotenoid biosyntheses were identified, respectively. Among these, chalcone synthase 2, chalcone isomerase 1, flavanone 3-hydroxylase 1, flavonoid 3′,5′-hydroxylase 1, dihydroflavonol 4-reductase 1, anthocyanidin synthase 1, and anthocyanidin 3-O-glucosyltransferase 1 were considered to be important in regulating the formation of blue petals, and phytoene synthase 1, phytoene desaturaser 1, ζ-carotene desaturase 1, lycopene β-cyclase 3, and β-carotene hydroxylase 2 might play important roles in orange sepal formation. This study improves our understanding of flower color and provides evidence for future molecular breeding of ornamental plants based on flower color modifications.