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Baicalein is a valuable flavonoid isolated from the medicinal plant <i>Scutellaria baicalensis</i> Georgi, which exhibits intensive biological activities, such as anticancer and antiviral activities. However, its production is limited in the root with low yield. In this study, In-Fusion and 2A peptide linker were developed to assemble <i>SbCLL-7</i>, <i>SbCHI</i>, <i>SbCHS-2</i>, <i>SbFNSII-2</i> and <i>SbCYP82D1.1</i> genes driven by the AtPD7, CaMV 35S and AtUBQ10 promoters with HSP, E9 and NOS terminators, and were used to engineer baicalein biosynthesis in transgenic tomato plants. The genetically modified tomato plants with this construct synthesized baicalein, ranging from 150 ng/g to 558 ng/g FW (fresh weight). Baicalein-fortified tomatoes have the potential to be health-promoting fresh vegetables and provide an alternative source of baicalein production, with great prospects for market application.