Complete nucleotide sequences of Tobacco leaf curl Japan virus (TbLCJV) isolates from infected tomato ( Lycopersicon esculentum) plants in Nara (-[Jp2], 2764 nt; -[Jp3], 2761 nt), Kochi (-[Koc], 2760 nt) and Yamaguchi (-[Yam], 2758 nt) Prefectures, of Japan were determined. These sequences were compared with each other and the sequences of further begomoviruses from Japan. TbLCJV, TbLCJV-[Jp2], TbLCJV-[Jp3], TbLCJV-[Koc], TbLCJV-[Yam], Honeysuckle yellow vein mosaic virus (HYVMV), Eupatorium yellow vein virus (EpYVV), EpYVV-[MNS2], EpYVV-[SOJ3], EpYVV-[Yam] and EpYVV-[Tob] are monophyletic. The intergenic region (IR) of TbLCJV has highest nucleotide sequence identity with that of HYVMV (93%) whereas the rest of the genomic DNA had higher identity with that of TbLCJV-[Jp2] or -[Jp3] (91 approximately 100%) than with that of HYVMV. In conclusion, TbLCJV has a chimeric genome which may have arisen by recombination between TbLCV-[Jp2] or -[Jp3]-like and HYVMV-like ancestors. Similarly, TbLCJV-[Yam] DNA has a hybrid genome, with a major parent HYVMV and minor parent TbLCJV-[Koc].