Sophora flavescens AITON kurara, has long been used to treat various diseases. Although several research findings revealed the biosynthetic pathways of its characteristic chemical components as represented by matrine, insufficient analysis of transcriptome data hampered in-depth analysis of the underlying putative genes responsible for the biosynthesis of pharmaceutical chemical components. In this study, more than 200 million fastq format reads were generated by Illumina's next-generation sequencing approach using nine types of tissue from S. flavescens, followed by CLC de novo assembly, ultimately yielding 83325 contigs in total. By mapping the reads back to the contigs, reads per kilobase of the transcript per million mapped reads values were calculated to demonstrate gene expression levels, and overrepresented gene ontology terms were evaluated using Fisher's exact test. In search of the putative genes relevant to essential metabolic pathways, all 1350 unique enzyme commission numbers were used to map pathways against the Kyoto Encyclopedia of Genes and Genomes. By analyzing expression patterns, we proposed some candidate genes involved in the biosynthesis of isoflavonoids and quinolizidine alkaloids. Adopting RNA-Seq analysis, we obtained substantially credible contigs for downstream work. The preferential expression of the gene for putative lysine/ornithine decarboxylase committed in the initial step of matrine biosynthesis in leaves and stems was confirmed in semi-quantitative polymerase chain reaction (PCR) analysis. The findings in this report may serve as a stepping-stone for further research into this promising medicinal plant.Key words Sophora flavescens; RNA-Seq analysis; biosynthesis; quinolizidine alkaloid; isoflavonoid Sophora flavescens AITON kurara, has been recorded and used for more than 1800 years. 1) As a widely distributed and effective herbal medicine, it severed as a cure for asthma, sores, gastrointestinal hemorrhage, diarrhea, allergy, inflammation in eastern Asian countries.2,3) Main chemical components of S. flavescens include flavonoids (1.5%), alkaloids (3.3%), alkylxanthones, quinones, triterpene glycosides, fatty acids as well as essential oils and recently, several clinical studies reported that alkaloids of S. flavescens were efficacious in treating various types of solid tumors (including breast, lung, liver and gastrointestinal tract cancers), which drew close attention to this traditional herbal plant. 1,4) In 1889, the characteristic compound matrine was isolated from the dry roots of S. flavescens by Nagai 5) and then in 1966, Okuda et al. confirmed the absolute structure of (+)-matrine.6) Due to its notable medicinal efficacy, attempts to synthesize and biosynthesize matrine were conducted. [7][8][9] In 1995, Saito et al. proposed the biosynthetic pathway of the carbon framework of matrine. 10) Although the first steps of quinolizidine alkaloids biosynthesis have been elucidated recently in S. flavescens, 11) more effort needs to be done to puzzle out the practical biosyn...