The complete nucleotide sequences of begomoviruses from pepper with leaf curl and yellowing symptoms, tomato with leaf curl symptoms, and ageratum with yellow vein in Indonesia were determined. On the basis of genome organization and sequence homology, they were proposed to belong to a new species, Pepper yellow leaf curl Indonesia virus (PepYLCIV), which includes the new strains PepYLCIV-Tomato and PepYLCIV-Ageratum. These viruses had bipartite genomes. Pepper virus DNAs from Indonesia (PepYLCIV, PepYLCIV-Tomato and PepYLCIV-Ageratum DNA-As) were noticeably distinct, forming a separate branch from the viruses infecting pepper. Considerable divergence was observed in the common region (CR) of the genomic components of PepYLCIV (77%), PepYLCIV-Tomato (82%) and PeYLCIV-Ageratum (75%). A stem-loop-forming region and a Rep-binding motif were identical in the CR of the three viruses. The CRs of PepYLCIV-Ageratum DNA-A was approximately 10 nucleotides longer than that of PepYLCIV DNA-A and PepYLCIV-Tomato DNA-A. A similar insertion was also found in the CR of PepYLCIV-Ageratum DNA-B. PepYLCIV DNA-A alone was infectious in pepper and Nicotiana benthamiana plants, and association with DNA-B increased symptom severity.