Abstract: Rehmannia glutinosa belongs to the Scrophulariaceae family with important medicinal value. In order to effectively explore the transcriptome information of R. glutinosa and identify the genes encoding enzymes involved in phenylethanol glycoside (PhGs) biosynthesis, the leaves, stems and tuberous roots of R. glutinosa were used for transcriptome sequencing using Pacific Biosiences RS II platform. A total of 27 773 transcripts were generated with an average length of 2 380 bp, and 27 236 coding sequences (CDS) were predicted. Using BLAST software, non-redundant transcript sequences were annotated with NR, NT, GO, COG, KEGG, SwissProt and Interpro databases and a total of 27 399 annotated genes were obtained. Among them, the number of genes related to Sesamum indicum in the NR database was the highest (81.44%), which is consistent with their evolutionary relationship. Enzymes likely involved in the biosynthesis of isoacteoside, echinacoside, cistanosides A, cistanosides F, 2'-acetylacteoside and leonoside F were identified, and 143 genes were identified in R. glutinosa full-length transcriptome. The expression levels of 19 genes correlated with acteoside content in twelve tissues of R. glutinosa, and most showed higher expression levels in leaf tissues and floral organs. This study provides more reliable transcriptome data for screening R. glutinosa for functional genes and provides a foundation for the study of the molecular mechanisms of PhGs biosynthesis.