Flower breeders are continually refining their methods for producing high-quality flowers.Phalaenopsisspecies are considered the most important commercially grown orchids. Advances in genetic engineering technology have provided researchers with new tools that can be used along with traditional breeding methods to enhance floral traits and quality. However, the application of molecular techniques for the breeding of newPhalaenopsisspecies has been relatively rare. In this study, we constructed recombinant plasmids carrying flower color-related genes,PhalaenopsisChalcone synthase (PhCHS5) and/or Flavonoid 3′,5′-hydroxylase (PhF3′5′H). These genes were transformed into bothPetuniaandPhalaenopsisplants using a gene gun or anAgrobacterium tumefaciens-based method. Compared with WT,35S::PhCHS5and35S::PhF3′5′Hboth had deeper color and higher anthocyanin content inPetuniaplants. Additionally, a phenotypic comparison with wild-type controls indicated thePhCHS5orPhF3′5′H-transgenicPhalaenopsisproduced more branches, petals, and labial petals. Moreover,PhCHS5orPhF3′5′H-transgenicPhalaenopsisboth showed deepened lip color, compared with the control. However, the intensity of the coloration of thePhalaenopsislips decreased when protocorms were co-transformed with bothPhCHS5andPhF3′5′H.The results of this study confirm thatPhCHS5andPhF3′5′Haffect flower color inPhalaenopsisand may be relevant for the breeding of new orchid varieties with desirable flowering traits.