Abstract: OBJECTIVE To explore the genetic basis of the biosynthesis of the swertiamarinin in S. mileensis. METHODS The high throughput sequencing by Illumina Hiseq 2500 was used to sequence its transcriptome of S. mileensis. RESULTS A total of 685 643 unigenes were assembled with an average length of 901 bp. Among them, 42 954 unigenes were annotated in the public databases NR, SwissProt, COG, KOG, GO and Pfam. The results showed that 43 unigenes were involved in the production of intermediate, 3 unigenes catalyze synthesis of terpenoids skeleton, and 25 unigenes might participate in terpene post-modification in the three steps of biosynthesis of swertiamain. CONCLUSION This study is the first comprehensive study on transcriptome of S. mileensis, and candidate genes involves in the biosynthesis of swertiamarin are obtained. The transcriptome data constitutes a much more abudant genetic resource that can be utilized to benefit further molecular biology studies on S. mileensis.