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<i>Ornithogalum dubium</i> is a popular ornamental monocot native to South Africa with flower colors ranging from pure white to deep orange. Gene editing based on the CRISPR/Cas9 system has recently been shown to hold potential for color improvement in ornamental flower crops. To apply this approach to <i>Ornithogalum</i> color manipulation, genomic or transcriptomic data must first be collected. Here, cDNA libraries of <i>O. dubium</i> leaves and flowers were constructed and sequenced using the Illumina HiSeq 2500. Over 155 million 100-bp paired-end reads were assembled into a transcriptome database of 360,689 contigs, of which 18,660 contigs were differentially expressed between leaves and flowers. Carotenoids are the main pigment imparting spectrum of orange hues to <i>O. dubium</i> flowers. By querying our database, we identified a total of 16 unique transcripts (unigenes) predicted to be involved in the carotenoid biosynthesis pathway of <i>Ornithogalum</i>. Combining carotenoid profiles, we further inferred several key unigenes responsible for floral coloration and accumulation in <i>O. dubium</i>, of which the gene LCYB/comp146645_c0 was found as a suitable target to generate potentially red flower varieties of <i>O. dubium</i>. Our research thus provides a framework for the application of CRISPR/Cas9 technology to improve this ornamental crop.