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Gene function analysis is challenging for Lilium due to the lack of an efficient method for stable genetic transformation. Virus-induced gene silencing (VIGS) is an attractive tool for determining gene function in plants. This study reported that Tobacco rattle virus (TRV)-based VIGS of a PHYTOENE DESATURASE (PDS) ortholog (LhPDS) can be achieved in Lilium × formolongi seedlings, with a survival rate of 92％, using the inoculation method of rubbing plus injection. Compared with untreated and mock-treated seedlings, the photobleached leaf phenotype of silenced plants significantly correlates with down-regulation of endogenous LhPDS (P ≤ 0.05). In addition, the silencing phenomenon can be observed in the growing points of plants, indicating that systemic viral infection was achieved using the protocol. The results indicate that TRV-based VIGS can be used to characterize gene function in Lilium × formolongi. This work lays the foundation for gene function analysis and molecular breeding in Lilium spp.