Cotton leaf curl disease is a major threat to cotton production in tropical and subtropical regions of the world. Begomoviruses are whiteflies-transmitted single-stranded DNA viruses belonging to the family Geminiviridae thatcause leaf curl disease in cotton. In present study, a strain of tomato leaf curl betasatellite and Xanthium strumarium alphasatellite have been found associated with Cotton leaf curl Kokhran virus in Gossypium hirsutum. A begomovirus and associated molecules were amplified, cloned and sequenced. Partial sequence analysis for begomovirus showed 98.2% sequence identity with an isolate of Cotton leaf curl Kokhran virus (HQ257374). The partial sequence of betasatellite showed highest sequence identity of 96.4% with tomato leaf curl betasatellites (EF068245, FR819710). The complete sequence for alphasatellite showed 98.2% sequence identity with Xanthium strumarium alphasatellite (HF547408). This is the first report that tomato leaf curl betasatellite have been found in cotton and after second epidemic of cotton leaf curl disease this is the first report of parent strain of Cotton leaf curl Kokhran virus in the field.