Andalusia, southern Spain, is a major horticultural production region within the Mediterranean, where over 10,000 ha are dedicated to the production of pepper (Capsicum annuum L.). Approximately two-thirds of the area dedicated to this crop is in a greenhouse and the remaining one-third is comprised of open field crops. Using pepper as a model, we identified and compared the major diseases caused by viruses in the different geographic regions and agronomic systems within the region. Pepper crops in plastic-covered greenhouses were predominantly associated with arthropod-transmitted virus diseases, such as TSWV. CMV was predominant in provinces located inland, and PMoV was found independent of the agrosystem, disease control methods, or geographic location.