Tomato crop is highly susceptible to various viral pathogens that pose significant economic implications. Egypt is the world’s fifth largest producer of tomatoes, employing thousands of families. In this study, 190 tomato samples, showing different types of symptoms, were collected from several Egyptian regions, and tested by qPCR for the presence of nine important viruses and viroids that infect this crop. Molecular analysis showed that Tomato brown rugose fruit virus (ToBRFV), Tomato yellow leaf curl virus and Tomato chlorosis virus were present in different tomato varieties and regions of Egypt, with different levels of infection. This study also described the biotypes of six Bemisia tabaci (B. tabaci) populations in five different tomato growing governorates, through the analysis of the mitochondrial genes COI. While Biotype B has already been reported in Egypt, the molecular assays used in this study showed the presence of three new subgroups of B. tabaci (Q1, Q2, and Q3), previously undocumented in Egypt, particularly in the governorates of Sharqia, Fayoum, and Beheira. The detection of B. tabaci populations belonging to Biotype Q, which is more aggressive than Biotype B, due to its resistance to a wide range of insecticides, causes potential threats of Tomato yellow leaf curl virus (TYLV) outbreaks in the country. This research provided valuable insights into the intricate dynamics of tomato production, viral pathogens, and B. tabaci populations, providing critical knowledge to propose integrated pest management for this crop in the country.