Begomoviruses are a serious threat cotton production throughout the world. In Pakistan, enormous crop losses occur as a result of cotton leaf curl disease [CLCuD] caused by begomoviruses. Molecular characterization of begomoviruses has made possible the identification and analyze of begomoviruses prevalent in a host plant. Infected cotton leaf sample [C-59] was obtained from area around Khanewal during 2011. The total DNA was isolated from the infected sample by cetyl trimethyl ammonium bromide CTAB method. An expected size band of approximately 1100 bp, covering coat protein region of the virus, was amplified using universal primers. The amplified product was T/A cloned and sequenced to its entirety. DNA sequence showed 99% nucleotide sequence identity to each of cotton leaf curl Burewala virus [ [CLCuBuV; accession No HF549184] and cotton leaf curl Kokhran virus [ [CLCuKV; accession No AJ002449] . Since CLCuBuV is a recombinant of CLCuKV and cotton leaf curl Multan virus and the coat protein virus region of CLCuBuV was derived from CLCuKV that is most probable reason that the available sequence showed identity with CLCuBuV as well as CLCuKV. A complete characterization of full length virus will determine whether isolate C-59 is CLCuBuV or CLCuKV. Literature indicates that there is no existence of CLCuKV within the region and CLCuBuV is dominating within Indo-Pak