Tomato yellow leaf curl Virus (TYLCV) threatens the production of tomatoes both in Egypt and the world. A virus was isolated from naturally infected tomato and pepper plants, grown in different areas in Egypt. The investigated isolate was characterized using electron microscopy, serology, biological tests, and polymerase chain reaction (PCR) using degenerate primers were used to amplify partial sequences (~530 bp) of the begomovirus coat protein gene (Cp) from samples of diseased plants. DNA sequence analyses of Egyptian isolate revealed high nucleotide sequence identities to isolates of TYLCV (99%) in GenBank. TYLCVEG encodes to 176 amino acids residues with MW 19.651 KDa. Twenty amino acids were detected of TYLCV-EG starting with Alanine (A) and ending with Tyrosine (Y). Phylogenetic analysis of Cp gene sequence of TYLCV-EG suggesting that the sequence variations observed in this isolate and some of those identified and published on GenBank may be attributable to intra-specific recombination events involving some TYLCV isolates. The great variability of the TYLCV isolates worldwide should be considered when breeding programs for virus resistance are established. A tomato line tolerant/resistant to a particular TYLCV isolate may not be as effective against another distantly related virus isolate.