Many viral diseases threaten the sustainable production of tomato (Solanum lycopersicum) and pepper (Capsicum annuum), which are among the most produced vegetables in the world and Türkiye. Eskişehir province of Türkiye produces a significant amount of vegetables both in the greenhouse and in the open-field. However, there have been no previous comprehensive study on the presence of viruses in tomato and pepper fields. In this study, 123 of 170 samples (72.4%) collected from tomato and pepper fields in Eskişehir in 2019 were infected with different viruses listed. While Orthotospovirus tomatomaculae (tomato spotted wilt virus, TSWV), cucumber mosaic virus (CMV), potato virus Y (PVY), tomato mosaic virus (ToMV), tobacco mosaic virus (TMV) viruses were detected by DAS-ELISA, pepino mosaic virus (PepMV), tomato chlorosis virus (ToCV) and tobacco necrosis virus (TNV) viruses could not be detected in both host plants. To molecularly characterize the selected isolates, the complete nucleocapsid (N) gene region specific to TSWV and a partial capsid protein (CP) gene region specific to CMV were amplified via RT-PCR, followed by sequencing. Phylogenetic trees were constructed with NCBI GenBank isolates and newly sequenced isolates. Genetic structure-related analyses such as genetic diversity, genetic differentiation, gene flow, neutrality tests, selection pressure, and recombination were performed on populations. In the phylogenetic tree of the TSWV N gene, the isolates are divided into three clades of geographical origin. Genetic structure analyses revealed that TSWV populations exhibited genetic diversity. In the phylogenetic tree of the CMV CP gene, the isolates are divided into known subgroups. The analyses indicate the presence of high genetic diversity and suggest that Subgroup IB, one of the clades, may contain subgroups within itself. In addition, there are indications for the existence of different CMV subgroups in Türkiye. Although different approaches were used for both the TSWV N gene and CMV CP gene, no recombination event could be detected. This study, marking the initial identification of viruses in tomatoes and peppers within the Eskişehir region, is believed to hold substantial potential for advancing future research endeavors and enhancing disease management not only within Türkiye but also globally.