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The growing problem of damage caused by Begomoviruses in economically important crops has generated a considerable ecological, social and cultural impact. Their incidence and severity is becoming increasingly alarming in different agricultural production systems, with tomato as the main host. Due to this, over several years, molecular and genetic techniques have emerged aimed at precisely understanding the mechanisms of action and response that take place during the plant-virus interaction. The aim is to elucidate the processes involved in the physiological expression of the plant and the pathogen, and from this, to counteract, inhibit, mitigate and/or eliminate diseases transmitted by this and other types of viruses. This monographic document presents basic information on the characteristics of Begomoviruses, their mechanism of infection and the current molecular techniques grouped within the "omics" tools for the management and control of these pathogens. It is hoped that this document can be useful in the understanding of the main viral diseases of plants.