Background : Momordica charantia L. (M. charantia) is a member of the family Cucurbitaceae, used as a medicine herb in traditional medicine. In this study, we present the sequencing, de novo assembly and analysis of the transcriptome of M. charantia and provide a global description of relationship between putative phenylpropanoid and flavonoid biosynthesis genes and alteration of phenylpropanoid and flavonoid content during different organs and plantlet of M. charantia. Methods and Results : The transcriptome of M. charantia was constructed by using an Illumina Nexteseq500 sequencing system. Out of 68,073,862 total reads, approximately 88,703 unigenes were identified with a length of 898 bp. Alternatively, transcriptomic data, 10cDNAs (McPAL, McC4H, Mc4CL, McCOMT, McCHS, McCHI, McF3H, McFLS, McDFR and Mc3GT) encoded phenylpropanoid and flavonoid biosynthetic genes. The expression levels and the accumulation of trans-cinnamic acid, benzoic acid, 4-hydroxyvbenzoic acid, p-coumaric acid, chlorogenic acid, caffeic acid, catechin hydrate, ferulic acid, and rutin were investigated in different organs and plantlets. Mainly, phenylpropanoids and flavonoids accumulated in leaves and flowers, whereas low levels accumulated in roots. Collectively, these results indicate that the putative McPAL, McC4H, McCOMT, McFLS, and Mc3GT might be key factors for controlling phenylpropanoid and flavonoid contents in M. charantia. Conclusion : In this study, we present the sequencing, de novo assembly and analysis of the transcriptome of M. charantia. We also compared gene expression and compound analysis of phenylpropanoid and flavonoid in different organs and plantlet of M. charantia. These results indicate that McPAL, McC4H, McCOMT, McFLS, and Mc3GT are key regulators of phenylpropanoid and flavonoid accumulation in M. charantia