The Feed the Future Innovation Lab for Integrated Pest Management (IPM-IL) funded by USAID is conducting adaptive research to mitigate crop losses due to viral diseases in subsistence agriculture in Nepal. Surveys were conducted in farmers’ fields in different regions of Nepal to document viruses affecting the production of vegetable crops. Symptomatic samples suspected for virus infections were collected and tested for specific viruses by serological and molecular diagnostic assays. Symptomatic samples from representative crops were imprinted onto FTA^TM PlantSaver Cards in the field, air dried and processed in the lab for virus testing. In addition, total RNA extracted from symptomatic samples was subjected to high-throughput sequencing for identification of viral sequences. The results indicated the presence of viral sequences highly similar to Bean common mosaic virus in beans, Zucchini yellow mosaic virus and Zucchini tigré mosaic virus in squash, pumpkin, bitter gourd and snake gourd, Potato virus Y (PVY) and Potato virus M in potato, PVY, Cucumber mosaic virus, Peanut bud necrosis virus, Tomato chlorosis virus and Tomato leaf curl New Delhi virus in tomato, Chilli veinal mottle virus in chillies, Bhendi yellow vein mosaic virus in okra and Turnip mosaic virus in broadleaf mustard. This knowledge is currently being used for in-country capacity building to implement integrated pest management strategy for controlling viral diseases in vegetable crops.