Abstract Begomovirus infection has been reported to cause many important diseases on vegetable crops in Indonesia. This research was conducted to reconfirm the identity of Begomovirus infecting several host plants. Plant samples were taken from several DI Yogyakarta locations, i.e., Sleman, Kulon Progo, and Bantul. Amplification of virus target was carried out by PCR method using three primer pairs, i.e., SPG1/2, PepYLCIVA-F/A-R, and PepYLCIV B-F/B-R. Begomovirus DNA fragments were successfully amplified from all samples using SPG1/2 primers, which confirmed the presence of Begomovirus infection in chili, eggplant, cucumber, and weed plants. The nucleotide sequences analysis identified five species of Begomovirus, i.e., PYLCIV, ToLCNDV, LUYVVV, TYLCIV, and TYLCKaV; each has homology with sequences in GenBank 86.76% -98.12%, 96.11%, 94.36%, 95.48%, 90%-99.29%, respectively. Sequence analysis of DNA fragments amplified using PepYLCIV B-F/B-R specific primers confirms that the genome type of PYLCIV is bipartite. Furthermore, the data showed a double infection of PYLCIV with other Begomovirus species, i.e., with TYLCKaV in chili and eggplant, with TYLCIV and LUYVVV in weeds, and with ToLCNDV in cucumbers. A double infection or a mixture of several viruses can cause recombination, potentially leading to new virus strains.