Plant transformation vectors pBI121-antiPDS, pTRV2-PDS, and 1300flag-Ruby, each driven by the 35S promoter were constructed using antisense PDS(antiPDS), RUBY, and virus-induced gene silencing (VIGS)-mediated PDS silencing as reporter gene systems, respectively. Transient transformation of these vectors in tobacco and pepper was performed via Agrobacterium tumefaciens infiltration. The expression effects of the three reporter gene systems were evaluated based on the phenotypic outcomes resulted from transient expressions of antiPDS interference, VIGS, and RUBY. All three reporter genes systems were first validated in tobacco leaves and then introduced into pepper leaves. The results showed that each system produced discernible phenotypic changes in both species. Both VIGS and antiPDS effectively silenced PDS, leading to localized bleaching patches in infiltrated leaves. VIGS induced more extensive and systemic silencing, consistent with its viral propagation nature, whereas antiPDS caused only localized suppression without spreading. Transient expression of RUBY produced red pigmentation, which confined to the infiltration zones. Among the three reporter systems tested, VIGS-mediated silencing produced the most visually striking phenotype in both tobacco and pepper. However, the bleaching caused by PDS silencing impaired photosynthetic function, which consequently hindered the subsequent growth and regeneration of transformed tissues, thereby limiting its use to transient assays. In contrast, the RUBY system acts as a gain-of-function reporter without adverse effects on plant development, suggesting it is a more suitable visual marker for applications requiring stable genetic transformation in pepper.