: Torenia fournieri Lind. is an ornamental plant, popular for its numerous flowers and variety of colors. However, its genomic evolution, as well as the genetic and metabolic basis of flower color formation, remain poorly understood. Here we report a chromosome-level reference genome of T. fournieri comprising 164.4 Mb. Phylogenetic analysis revealed the phylogenetic placement of the species, and comparative genomics analysis indicated that T. fournieri shared a whole genome duplication (WGD) event with Antirrhinum majus . Through joint transcriptomics and metabolomics analyses, we characterized the differential genes and metabolites in the anthocyanin synthesis pathway in five T. fournieri varieties. We identified many metabolites related to pelargonidin, peonidin, and naringenin in Rose (R) color samples. On the other hand, the blue (B) and blue-violet (D) color samples contained many metabolites related to petunidin, cyanidin, quercetin, and malvidin. The formation of different flower colors in T. fournieri involves multiple genes and metabolites. We analyzed the results and obtained significantly different genes and metabolites related to the biosynthesis of flavonoids and anthocyanins, which are key metabolites in the formation of different flower colors. Our T. fournieri genome data provide a basis for studying the differentiation of this species and provide a valuable model genome enabling genetic studies and genomics-assisted breeding of T. fournieri . Highlight: The genome of Torenia fournieri was reported for the first time, and the formation mechanism of different colors in Torenia fournieri flowers was analyzed by genomics, transcriptomics and metabolomics.