It is important new text book, sharply focous on begomoviruses. It is first report from Pakistan. The sequences obtained in this study were compared with reported sequence in NCBI database using BLAST analysis and preliminary results showed that clone FQ-1 is a strain of MeYVMV and FQ-2, FQ-3 and FQ-4 are isolates of AEV. Sequence FQ-1 were downloaded and used for sequence comparison in MegAlign by Clustal V method. MegAlign results showed that clone FQ-1 has between 89.9 and 91.9% identity to MeYVMV. It encodes six ORF typical of Old World begomoviruses. The complete sequence of FQ-1 is submitted to NCBI databank under accession no. HE578897. Phylogenetic analysis showed that sequence of obtained in this study has a distinct position in the phylogenetic tree and it appears to be among the ancestors of already reportd MeYVMV. In multiple alignment the comparison of the IR sequence of MeYVMV (DNA-A) with that of other isolates of the species showed that it has a stem-loop structure (with a nonanucleotide TAATATTAC) and TATA box forming part of Rep promoter like other begomoviruses. There are three iterons (ACCGA/CT), F1 and F2 on virion-sense strand and R1 on complementary strand.