Plant viruses have become a major issue to the crop production around the world. These viruses have become an unavoidable limiting factor by causing rigorous crop deficit for those major crops which are economically important. Among these viruses, begomoviruses belonging to family Geminiviridae, have brought the major devastation to both monocots and dicots in tropical and sub-tropical regions. These begomoviruses are transmitted through white fly and cause diseases like mosaic, yellow mosaic, yellow leaf curling, and yellow vein etc. The objective of this study is to evaluate the association between the genetic diversity of begomoviruses and phenotypic data to identify the ideal cotton genotype for breeding. In this study, 30 leaf samples with CLCuD symptoms were analyzed using rolling circular amplification and PCR. Obtained results expressed the presence of begomovirus with its associated satellites (i.e. alpha and betasatellites) in six varieties, association of begomovirus and betasatellites in four varieties and combination of begomovirus with alphasatellite in six varieties. Severe disease symptoms were exhibited with these combinations in selected varieties but betasatellite-begomovirus complex demonstrated a deadly impact. Few varieties expressed the resistance against the begomoviruses, so these varieties can further be manipulated for breeding.