Cymbidium longibracteatum is an economically important Chinese orchid well known for its silver- or gold-colored leaf color patterns, and is desired for its ornamental value. In this study, we analyzed the yellow and green rhizomes from C. longibracteatum by deep RNA-sequencing. A total of 333,497 transcripts and 162,407 unigenes of ‘longchangsu’ obtained from 39.59 Gb of clean reads. Differentially expressed gene (DEG) analysis indicated that 497 genes were upregulated and 147 downregulated in the leaf color mutant. Five of these DEGs were involved in the phototransduction pathway, and 48 genes belonged to the plant-pathogen interaction pathway. Furthermore, we identified seven genes associated with the photosystem, six of which were upregulated, and one (psbA) was downregulated. Our results showed that downregulation of psbA gene may produce leaf color mutants under certain culture conditions that affect the D1 protein of photosystem II. All seven genes were validated by qRT-PCR. This study on genes related to photosystem and other pathways establishes a genetic foundation for ornamental orchids and may help to improve the economic and breeding values of C. longibracteatum.