Tomato production in the Mediterranean region and elsewhere is under constant threat of the whitefly-transmitted begomoviruses that cause Tomato yellow leaf curl disease (TYLCD). Sequencing has indicated that the generic 'TYLCV' includes a large number of viruses and strains. We studied the distribution of the tomato yellow leaf curl disease-associated viruses in Egypt, Israel, Jordan and Lebanon. Two simple and reliable multiplex PCR protocols (mPCR) were developed that allowed the detection of Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) species, in addition to Tomato yellow leaf curl virus-Mild (TYLCV-Mld) strain. PCR products were sequenced to confirm their identity. The full-length genomes were also sequenced of TYLCV from Egypt, Jordan and Lebanon, TYLCV-Mld strain from Jordan and Lebanon, and Tomato yellow leaf curl Sardinia virus-Sicily from Israel. This is the first time that TYLCSV-Sic has been detected in Israel and Jordan, and the first report of TYLCV-Mld strain from Egypt and Lebanon.