Abstract: A prevalent trend in recent biological developments is the integration between ecology and evolutionary biology. To further investigate the integration, exploratory studies are needed for linking phenome to genome with suitable biological systems. Biochemistry of floral pigmentation and genetics of the anthocyanin pathway, including regulatory and structural genes in several model angiosperms, have made floral color a preferred trait for ecological and evolutionary research, which may lead to further understanding of how floral color varies among wild species. Our review focuses on the genetic, biochemical and ecological aspects of the anthocyanin pathway in Ipomoea (Convolvulaceae), to provide some background information on the natural variation of floral color from multi-disciplinary angles. We also discussed unsolved issues and possible future developments.