Weeds are usually considered as a source of new viruses but are often neglected during diversity studies. Previously eleven samples of weeds were collected along the edges of a tomato crop field located in four municipalities (Florida, Ginebra, Cerrito and Candelaria) in the Southeast of Valle del Cauca. These samples were positive for begomoviruses but their molecular characterization had not been done until now. For each sample, DNA fragments were cloned, sequenced and analyzed. Nucleotide sequence analysis of viral fragments showed the presence of six different begomoviruses: two virus isolated from Lantana camara, Desmodium sp. and Amaranthus dubius were previously described as potato yellow mosaic virus (PYMV) and passionfruit leaf distortion virus (PLDV), respectively; other four virus which were isolated from L. camara, A. dubius, Rivina humilis, Desmodium sp., Rhynchosia minima, Hybanthus attenuatus, Verbena sp., Croton hirtus and Caesalpinia sp., showed its highest nucleotide sequence identity (89%) with bean chlorotic mosaic virus (BChMV), datura leaf distortion virus (DaLDV) and rhynchosia golden mosaic Yucatan virus (RhGMYV). Cloned viruses fragments from these weeds could be new begomoviruses not previously reported before, this in accordance with the ICTV species demarcation criterion for the genus Begomovirus (≥91 % sequence identity). Mixed infections of begomoviruses in Desmodium sp. and A. dubius weeds also was found in this analysis. Finally, this paper reports by the first time to three alternative begomoviruses weeds hosts that infect tomato and passion fruit crops: A. dubius for PYMV, and L. camara and Desmodium sp. for PLDV, respectively.