Cotton is a most important crop (white gold) in Egypt. Cotton is attacked by leaf curl virus that members of the genus Begomovirus (Family: Gminiviridae) have circular single stranded DNA genomes, this virus that is transmitted by the whitefly (Bemisia tabaci). In the present study aims to detect the presence of Begomovirus in cotton representing leaf curl virus and identify the molecular characteristic of CLCuV using: Isolation of Replicative form (RF: 2.7 kbp), Specific PCR of coat protein gene (AV1), Cloning, Sequencing, Expression and Protein Purification. To achieve this purpose, four isolates of the virus were randomly collected from infected leaves of cotton from six localities in Egypt. The leaf isolates in the current study showed different gradients of typical symptoms of begomoviruses disease that appears upward or down ward leaf curling, thick dark green veins, vein swelling. In addition, study of genotyping for begomoviruses in differnt hosts such as (cotton, tomato,okra) using different techniques RAPD, SSCP, Phylogentic tree.