The genus begomovirusbelongs to the family Geminiviridae that have emerged as serious constraints worldwide and infect variety of crops including vegetables, ornamental plants and weeds. To determine the diversity of begomoviruses on chillies,samples were collected on the basis of symptoms from Attock, Talagang, Chakwal, Islamabad and Hyderabad. Samples were tested by TAS-ELISA against begomoviruses by use of monoclonal antibodies of African cassava mosaic virus (ACMV), Indiancassava mosaic virus (ICMV) and Okra leaf curl virus (OLCV). The results indicated that all isolates showed range of high to moderate or low level of reaction. A panel of four monoclonal antibodies of ACMV, three of ICMV and three of OLCV were used. Epitope profile pattern slightly differed within each group, depending upon the location and concentration of the virus in the tested isolates. It was also confirmed that symptomatic chilli samples contained multiple infections of the begomoviruses in the studied area. Diverse patterns were found indicating great diversity among begomoviruses infecting chillies. The core region was amplified using two sets of degenerate primers. The sequencing data of nineteen samples indicates the presence of nine different species of begomoviruses, namely;Chilli leaf curl virus (ChLCV),Mesta yellow vein mosaic virus (MYVMV), Tomato enation leaf curl virus (ToELCV), Tomato leaf curl Karnataka virus (ToLCKV),Tomato leaf curl Gujarat virus (ToLCGV),Papaya leaf curl virus (PLCV),Tomato yellow leaf curl virus (ToYLCV),Chilli leaf curl Oman virus (ChLCOV),Pedilanthus leaf curl virus(PeLCV).More than one virus was isolated from the single sample indicating 1 12 thepresence of mixed populations of begomoviruses in chilli crop. Full length genome of four different begomovirus species was obtained, (248)Pedilanthus leaf curl virus (PeLCV), (249)Cotton leaf curl Burewala virus (CLCuBV), Pepper leaf curlvirus (PepLCV) and (251)Tomato leaf curl Gujarat virus (ToLCGV). No evidence for the presence of DNA-B was available, using abutting primers from the Intergenic Region (IR), when the same samples were tested. This indicates the monopartite nature of begomoviruses isolates, associated with betasatellites and alphasatellites. It becomes clear that CLCuBV and PepLCVwere associated with PLCVβ and CLCuBα. However PeLCV possesses PLCVβ but there was no association of alphasatellites. Furthermore, ToLCGV was associated EYVβ; however, alphasatellite was absent. Apart from understanding the nature of mix infection, this study has both epidemiological and pathological implications. Diseases caused by begomoviruses and associated DNA satellites have been expanding rapidly both in geographical distribution and host range. Given the presence of large number of begomoviruses throughout Asia and Africa, and ability of DNA-β to substitute for DNA-B, the probability may exist that new species/strains of begomoviruses emerge. Any effort towards developing resistance to disease, either by conventional or nonconventional means would be wise to take into account the possibility of more complex situation becoming important in chilies in the future.