Background: Dendrobium plants are well known for their uses in traditional Chinese herbal medicine. Bibenzyl compounds are the main active compounds in Dendrobium officinale. However, the physiological and molecular basis for the biosynthesis of bibenzyl compounds in Dendrobium plants remains underexplored. Results: In this study, the accumulation of erianin and gigantol were studied as representative compounds of bibenzyl. Their presence in plant tissues were investigated. Our results show that root tissues contained the highest content of bibenzyl (erianin and gigantol). Based on the pre-experimental result that exogenous application of Methyl-Jasmonate promotes the biosynthesis of bibenzyl compounds in D. officinale root tissues, comparative transcriptomic analyses were conducted between the bibenzyl-accumulated root tissues and a control. In total, we identified 1,342 differentially expressed genes (DEGs) with 912 up-regulated and 430 down-regulated genes. Most of the identified DEGs are functionally involved in the JA signaling pathway and the biosynthesis of secondary metabolites. In particular, we identified 11 enzymatic genes functionally involved in bibenzyl biosynthesis.Conclusions: Our study provide insights on the identification of putative genes associated with bibenzyl biosynthesis and accumulation in Dendrobium plants, and also paves the way for future research on dissecting the physiological and molecular mechanisms of bibenzyl synthesis in plants as well as on how to best utilize genetic engineering and molecular modification techniques to genetically improve Dendrobium varieties by increasing the content of bibenzyl for drug production and industrialization. Keywords: Bibenzyl, D. officinale , Differentially expressed genes, Secondary metabolites, Transcriptome analysis.