Tomato spotted wilt virus (TSWV) is a formidable plant pathogen, inflicting severe economic losses in agriculture due to its broad host range and insect vector transmission. In this study, TSWV was identified in tomato plants in Muş province, Turkey, using molecular methods, and its coat protein (CP) gene was sequenced. The Muş 49 strain shared a remarkable 97% nucleotide similarity with global TSWV isolates and exhibited close phylogenetic relationships with strains from Turkey, Hungary, Bulgaria, and Serbia. Notably, the findings suggest that TSWV genetic diversity is independent of host plant species and geographic location. Beyond genetic characterization, the study explored the antiviral potential of natural stilbene compounds using in silico molecular docking. Remarkably, six of the 13 tested stilbenes exhibited stronger binding to TSWV CP than resveratrol, a well-known antioxidant. Among them, viniferin demonstrated the highest binding affinity (−8.6 kcal/mol), highlighting its promising antiviral potential. These findings suggest that stilbenes may effectively target conserved viral regions and serve as natural inhibitors against plant viruses. Future in vitro and in vivo research will be crucial to validating these promising antiviral candidates. This study not only uncovers new insights into TSWV genetic diversity in Turkey but also paves the way for harnessing natural compounds as innovative plant virus management strategies.