The orchids GL and YL are two cultivars of Cymbidium longibracteatum. YL displays an obviously yellowing rhizome and yellow leaves, while GL ('Longchangsu') shows dark green leaves and greenish rhizome. But the molecular mechanism for the differences between the two cultivars is poorly understood. In the present study, we showed that the structure of chloroplasts was significantly damaged in YL. Biochemical analysis uncovered the contents of chlorophyll a, chlorophyll b, total chlorophyll and carotenoid were notably decreased in YL. Using RNA-Seq technology, more than 38 million clean reads were generated in each pool, and 116,422 unigenes were assembled de novo. 6,660 unigenes with differential expression patterns (FDR≤0.01 and |log2 ratio|≥1) were totally identified between the two cultivars. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed unigenes (DEGs) suggested 33 KEGG pathways were notably enriched, including biological processes such as "phenylpropanoid biosynthesis", "phagosome", "starch and sucrose metabolism", "drug metabolism-cytochrome P450", "fatty acid elongation", and "flavone and flavonol biosynthesis". Further analysis revealed that chlorophyll degeneration related unigene (c48794_g1) and flavonoid biosynthesis related unigenes (c16388_g1, c48963_g1, c63571_g1, c4492_g1, c52282_g1, c78740_g1, c4645_g1) were up-regulated while carotenoid biosynthesis related unigene (c7212_g1) were down-regulated in YL. Additionally, six of NAC, R2R3-MYB, bHLH transcription factors (c42861_g1, c105949_g1, c61265_g1, c42659_g1, c82171_g1, c19158_g1) might be involved in regulation of pigment biosynthesis. The chlorophyll degeneration and the flavonoid biosynthesis related unigenes up-regulation together with the carotenoid biosynthesis related unigenes down-regulation may contribute to the yellowing phenotype of YL.