Our results demonstrated that the epidemics caused by begomoviruses in chilli crop is associated with a high level of complexity caused by the begomovirus species involved and the sequence diversity of the begomovirus species. It seems that these crops provide an environment with a high risk for further evolution of new begomoviruses via recombination. Available evidence suggests that these disease complexes are rapidly expanding in terms of their geographical distribution and host range. Future studies should address the epidemiological consequences of the observed virus diversity. Appearance of chilli leaf curl disease in such a great severity can be attributed to the synergistic action of geminivirus disease complex comprising a monopartite Pepper leaf curl Bangladesh virus and bipartite Tomato leaf curl New Delhi virus along with DNA β satellite component.