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Phalaenopsis is one of the world’s most popular and important epiphytic monopodial orchids. The extraordinary floral diversity of Phalaenopsis is a reflection of its evolutionary success. As a consequence of this diversity, and of the complexity of flower color development in Phalaenopsis, this species is a valuable research material for developmental biology studies. Nevertheless, research on the molecular mechanisms underlying flower color and floral organ formation in Phalaenopsis is still in the early phases. In this study, we generated large amounts of data from Phalaenopsis flowers by combining Illumina sequencing with differentially expressed gene (DEG) analysis. We obtained 37 723 and 34 020 unigenes from petals and labella, respectively. A total of 2736 DEGs were identified, and the functions of many DEGs were annotated by BLAST-searching against several public databases. We mapped 837 up-regulated DEGs (432 from petals and 405 from labella) to 102 Kyoto Encyclopedia of Genes and Genomes pathways. Almost all pathways were represented in both petals (102 pathways) and labella (99 pathways). DEGs involved in energy metabolism were significantly differentially distributed between labella and petals, and various DEGs related to flower color and floral differentiation were found in the two organs. Interestingly, we also identified genes encoding several key enzymes involved in carotenoid synthesis. These genes were differentially expressed between petals and labella, suggesting that carotenoids may influence Phalaenopsis flower color. We thus conclude that a combination of anthocyanins and/or carotenoids determine flower color formation in Phalaenopsis. These results broaden our understanding of the mechanisms controlling flower color and floral organ differentiation in Phalaenopsis and other orchids.