Several isolates of a novel begomovirus were characterized from tomato samples collected in northern Uruguay exhibiting disease symptoms associated with Bemisia tabaci infestations. Analysis of full-length sequences of DNA-A and DNA-B components revealed the presence of a new begomovirus with the typical genome organization of a New World begomovirus, for which the name tomato rugose yellow leaf curl virus (ToRYLCV) is proposed. A high degree of nucleotide sequence diversity was found for both components, suggesting the presence of a diverse virus population. Recombination analysis suggested relationships of ToRYLCV to begomoviruses reported from the New World. Although common regions from DNA-As and DNA-Bs were surprisingly divergent for a cognate pair, a DNA-A and DNA-B pair cloned from one sample were infectious in Nicotiana benthamiana and tomato and reproduced symptoms observed in field-infected tomato plants, suggesting that ToRYLCV is the causal agent of the disease observed. This is the first report of a begomovirus infecting tomato crops in Uruguay and of the presence of begomovirus in this country.