Analysis of plant viruses in the greenhouse production of vegetable crops in Russia shows that the introduction of new species with seeds and agricultural products from other regions and countries poses a significant risk to tomato and cucumber. The main challenge in detecting viral infections is the long incubation period and the need for technically advanced diagnostic methods. The successful development of immunological and molecular analysis techniques allows us to detect a wide range of new viruses, but the economic feasibility of these methods must be considered. To determine the minimum number of viruses that need to be diagnosed, we assessed all varieties of viruses that infect vegetables and the risk of their spread in greenhouses in Russia. We analyzed 56 samples of symptomless plants collected in routine assays of commercial greenhouses in the four regions of the Russian Federation in 2022-24 to identify the viruses that can cause potential damage to crop production. Plant samples were used to isolate RNA using the phenolic method. After DNase treatment, the quality and quantity of the RNA were tested using an Agilent 2100 bioanalyzer (Agilent). The preparation of the Illumina library and RNA sequencing was carried out at the Russian Plant Quarantine Center (VNIIKR, Moscow region), using TruSeq RNA. The Illumina libraries were quantified using the qPCR method, and the samples were sequenced using the Illumina HiSeq 2000. The analysis of the data from RNA sequencing (RNA-Seq) was conducted using the Taxonomer software. The following latent viruses were identified in most of the locations with a number of reads ranging from 0.01 to 0.11%: Pepper chlorotic spot virus, Zucchini lethal chlorosis virus, Physalis rugose mosaic virus, Chenopodium quinoa mitovirus 1, Tobacco vein-clearing virus, Dahlia mosaic virus, Pelargonium vein-banding virus and Longan witches’ broom-associated virus. While these detected plant viruses may not pose a significant risk to plants, their presence indicates that a viral infection is currently spreading from Latin America and Southeast Asia. These viruses can infect plants and remain active over a number of years, posing a potential threat to plant health. Climate change may contribute to the further spread of these viruses and their vectors in open field ecosystems. The increase in international trade of plant products has led to a greater risk of new viruses entering plant ecosystems.