Magnoliae officinalis is the plant source of houpo, a widely used traditional Chinese medicine to treat symptoms of gastrointestinal diseases. Its main active components, magnolol(MG) and honokiol(HK), have excellent pharmacological actions, but little research has focused on the functional genes involved in the MG and HK metabolic pathways. In this study, using RNA-seq and gene expression profile, we present the first transcriptome characterization of M. officinalis leaves, twigs and stems.Based on similarity search against nonredundant protein databases, 30,660 contigs had at least a significant alignment to existing public database. Pathway analysis showed that 8707 contigs were assigned to 317 KEGG pathways. A second skeleton pathway with 14 putative homologous genes was also identified as involved in lignan biosynthesis. Expression profiles of these 14 genes showed that leaves and twigs seem to have higher transcript levels for lignan components than in stem tissue; this result was then verified by q RT-PCR. Our work will immensely facilitate metabolic research on lignan biosynthesis in M.officinalis. Magnoliae officinalis is the plant source of houpo, a widely used traditional Chinese medicine to treat symptoms of gastrointestinal diseases. Its main active components, magnolol (MG) and honokiol (HK), have excellent pharmacological actions, but little research has focused on the functional genes involved in the MG and HK metabolic pathways. In this study, using RNA-seq and gene expression profile, we present the first transcriptome characterization of M. officinalis leaves, twigs and stems.Based on similarity search against nonredundant protein databases, 30,660 contigs had at least a significant alignment to existing public database. Pathway analysis showed that 8707 contigs were assigned to 317 KEGG pathways. A second skeleton pathway with 14 putative homologous genes was also identified as involved in lignan biosynthesis. Expression profiles of these 14 genes showed that leaves and twigs seem to have higher transcript levels for lignan components than in stem tissue; this result wa s then verified by q RT-PCR. Our work will immensely facilitate metabolic research on lignan biosynthesis in M. officicinalis.