Abstract: Lilium ‘Siberia’, a typical and fragrant oriental hybrid lily, emits a large amount of monoterpenes, which shows considerable developmental emissions. To date, however, the mechanisms for this remain largely unknown. In this study, we used RNA sequencing (RNA-seq) to determine the petal transcriptome at four different flowering stages, including bud (BS), half-bloom (HS), full-bloom (FS), and late-bloom stages (LS), and analyzed differentially expressed genes(DEGs)to investigate the molecular mechanism of monoterpene biosynthesis. Based on the transcriptome sequencing, we obtained 56.28 Gb of clean bases and 223.40 Mb of clean reads, which were assembled into 124 233 unigenes, 35 749 of which were annotated. The genes in the terpenoid backbone biosynthesis pathway showed significantly different expression at different flowering stages. The gene expression levels of 1-deoxy-D-xylulose 5-phosphate synthase(DXS),1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (HDS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), and geranyl diphosphate synthase (GPS) first increased and then decreased with flowering stage. The gene expression of ocimene synthase (OCS) exhibited a similar pattern, with a maximum at FS, consistent with monoterpene emission in our previous study. The gene expression of HMG-CoA reductase (HMGR) in the mevalonate (MVA) pathway also presented the same pattern; however, the gene expression patterns of solanesyl-diphosphate synthase (SDS) and geranylgerany1 diphosphate reductase (GGDR) showed the opposite trend and were the lowest during FS in the branched pathway downstream of monoterpene biosynthesis. We demonstrated that the gene expression of key enzymes in the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway regulated the biosynthesis of monoterpenes with flower development, resulting in high release during FS. Moreover, the high activation level of the MVA pathway and the depressed branched metabolic pathway of ubiquinone and other terpenoid-quinones during FS may partly contribute to monoterpene biosynthesis.