 Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae).  A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. More than 10% of the novel genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait.  Other contrasting gene expression between flowers included that related to flower development and color, hormones, and iridoid biosynthesis. Metabolomic analyses similarly suggested differential concentrations of both hormones and iridoids in the two types of flowers. The interactions between multiple genes may together lead to contrasting morphology and open versus closed pollination of the dimorphic flowers in this species.  A total of 56 candidate genes were identified from the known iridoid biosynthesis-related pathways. Two hub genes were found to play an essential role in transferring intermediate products between leaves and flowers during iridoid biosynthesis.