Total DNA extraction was carried out from the five virus infected host plant species namely, Zinnia elegans, Eclipta prostrata, Solanum nigrum, Capsicum annuum and Ageratum conyzoides with suspected Geminivirus symptoms. By using universal primers for the DNA A genome of whitefly-transmitted geminiviruses, approximate full length DNA A genome was PCR amplified for four of the viruses Zinnia leaf curl virus (ZiLCV), Solanum yellow leaf curl virus (SYLCV), Pepper leaf curl virus (PeLCV) & Ageratum yellow vein virus-Pakistan (AgYVV-P) except Eclipta prostrata yellow vein virus (EPYVV). Nucleic acid hybridization was used to compare homologies with four different probes of the begomoviruses namely african cassava mosaic virus (ACMV), watermelon chlorotic stunt virus (WCSV), cotton leaf curl virus (CLCuV) and SYLCV (DNA A). Relative levels of cross hybridization were analyzed under similar optimized conditions for each test. EPYVV showed least homology with any other Begomovirus from Pakistan, PeLCV found to be more closely related with ACMV and WCSV as compared to the probes from Pakistan viruses ie., SYLCV & CLCuV.