The Tomato Chlorosis Criniviruses (ToCV) and Tomato yellow leaf curl Geminivirus (TYLCV), which naturally infecting and limited to the phloem, have caused a drastic reduction in tomato yield. The current study aims to determine the incidence of single and mixed viruses using biological, serological and molecular PCR methods in natural tomato plants. The incidence of mixed infection was found more frequently, followed by ToCV and TYLCV (42.3, 28.8, 17.8 in 2020 and 49.1, 29.7 and 19.1% in 2021, respectively). ToCV causes chlorosis, TYLCV causes leaf curl and yellowing, while mixed ToCV & TYLCV cause progress symptoms. By using the heat shock protein 70 (HSP70) and coat protein (CP) genes, ToCV and TYLCV isolates could be identified. These isolates were recorded in GenBank under accession codes "ON951644.1" and "OP265136.1" respectively. Host plants responded differently to severe and common disease density between ToCV and TYLCV. The transmitted whitefly could distinguish between ToCV and TYLCV within 15-20 minutes of the acquisition period. ToCV increases in fields with high whitefly populations, requiring further research to understand effects and reduce harm.