Two species of Goji, Lycium barbarum L. and Lycium ruthenicum Murr., are novel functional vegetables and functional fruits widely used in China and other Asian countries. Both species possess complex secondary metabolic pathways and show high tolerance and adaptability to saline-alkali stress, making them novel targets for functional genetic analysis of the biochemical pathways involved. Although stable transgenic Goji lines have been produced, the process is very labor-intensive and time-consuming. Virus-induced gene silencing (VIGS) presents an effective and rapid alternative for creating targeted gene knock-outs to study gene function in plants. In this study, the first application of VIGS in Lycium species is presented, using the Tobacco rattle virus (TRV) vectors. A number of vector delivery methods were trialed, including leaf syringe-infiltration, agrodrench, seedling vacuum-infiltration and sprout vacuum-infiltration (SVI).Vacuum-infiltration was the most effective method and was used to successfully silence two reporter genes, phytoene desaturase (PDS) and Mg-chelatase H subunit (Chl H), concomitant with photobleaching and yellow leaf phenotypes, respectively. The proven application of VIGS to these Lycium sp. will expedite the functional characterization of novel genes involved in the biosynthesis of functional components both in leaves and fruits, as well as the abiotic stress tolerances.