The importance of diseases of tomato caused by begomoviruses is increasing worldwide. Here, we report that several begomoviruses are associated with tomato leaf curl disease in Yunnan province, China. 14 tomato samples showing leaf curl symptoms were collected in three districts in Yunnan, and they fell into four groups according to their reaction with a panel of 16 monoclonal antibodies in TAS-ELISA. Comparison of partial DNA-A sequences amplified with degenerate primers confirmed the existence of several types of begomoviruses. The complete DNA-A sequences of 4 isolates (Y25, Y41, Y72, Y161), corresponding to the four groups, were determined. Sequence comparisons and phylogenetic analysis revealed that they corresponded to four previously identified begomoviruses. Groups I, II and IV are most closely related to Tomato yellow leaf curl China virus (TYLCCNV), Tobacco curly shoot virus (TbCSV) and Tobacco leaf curl Yunnan virus (TbLCYNV), respectively, while Group III shows close relationships with Tomato yellow leaf curl Thailand virus (TYLCTHV). In addition, all isolates in Groups I and III were found to be associated with DNAbeta molecules, while satellite DNA was not found in virus isolates in Groups II and IV. The complete DNAbeta sequences of three isolates from Group III (Y72, Y77, Y79) were determined. Sequence analysis showed that Y72beta, Y77beta and Y79beta seem to be different from other characterised DNAbeta, sharing the highest nucleotide sequence identity with DNAbeta of TbCSV.