The world’s population is growing, and with it, the demand for food is increasing exponentially. Tropical and subtropical fruit crops are important for the consumer chain. The emergence of epidemic viruses has turned the production and marketing of papaya (Carica papaya L.), avocado (Persea americana Mill.), banana (Musa spp. L.), and citrus fruits (Citrus spp.) upside down, to the point that they are threatened by the presence of important viruses. This chapter presents a classification of viruses that affect fruit trees, including the genera: Closterovirus, Ampelovirus, Crinivirus, Bymovirus, Ipomovirus, Macluravirus, Rymovirus, Badnavirus, and Begomovirus. Viral transmission in trees depends on the epidemiology of the virus, with most being transmitted by arthropods, grafts, and infected rootstocks. The fundamental basis for achieving efficient integrated management begins with the establishment of a structured epidemiological surveillance system, including third-generation early diagnosis tools to prevent the spread of emerging viruses. So far, success has been based on advances in surveillance rather than on virus control itself. The main strategy may be based on controlling the risk posed by viruses, rather than on stopping their emergence in fruit crops.