Several viruses infect cotton plant across the globe. Due to climate change, which favors the insect’s growth and reproduction, the diseases transmitted by insect vectors are increasing at alarming rate. The viruses causing leaf curl disease are common in Africa and Asia. Cotton crop is infected by single stranded DNA viruses (Family, Geminiviridae) in Pakistan. It was originally limited to Pakistan, but now it has spread to India, China and Philippines. In the New World a virus causing leaf crumpling is known to infect cotton. The studies in this thesis were aimed at a clearer understanding of the virus species responsible for the CLCuD complex and possible reasons it became an epidemic. These single stranded DNA viruses were surveyed, isolated and amplified with a novel one step PCR protocol to identify the major three viruses, namely cotton leaf curl Multan virus, cotton leaf curl Kokhran virus and Burewala strain of Kokhran virus. Furthermore, PCR and RCA was used to quickly cloned and sequenced full-length viruses and satellites from cotton and alternate host tomato plants to estimate the extent of diversity of begomoviruses in Punjab. The sequence analysis revealed that viruses co-circulating in cotton and tomato plants but may only create diseases in one host. Furthermore, these viruses are harboring several distinct satellites. The mutation and recombination analysis revealed that cotton leaf curl geminiviruses (just like RNA viruses) have a high and specific pattern of recombination and mutation and favored a combination of viral molecules, which have the capacity to spread at higher rate compared to other strains of cotton leaf curl geminiviruses. In this manuscript, the diversity and spread of cotton leaf curl disease is discussed in depth to understand the viral evolution in Pakistan, uses for host plant resistance, and implicated for research and management strategies to prevent new epidemics worldwide.