The tomato is one of the most important vegetable crops. The successful development of tomato cultures in Kazakhstan depends on the implementation of intensive agricultural methods, including breeding and selecting for new tomato varieties resistant to plant pathogens. Common tomato viruses, although not detected in our country to date, may potentially have a deleterious impact on agriculture if allowed to spread. The implementation of tomato breeding programs based on molecular markers of resistance is therefore an important preventive measure for protecting the agriculture and food safety of Kazakhstan. In the present work, we used nine molecular markers associated with resistance to three tomato viruses, i.e., tomato mosaic virus (ToMV), tomato spot wilt virus (TSWV), and tomato yellow leaf curl virus (TYLCV), to test the local breeding collection for the presence of genetic resistance factors. Two tomato varieties, ‘Zhiraf’ (Russia) and ‘Sunnik’ (Armenia), were revealed to possess the resistant allele marker PrRuG86-151 against ToMV; three hybrid forms had the same allele in the heterozygous state. One hybrid, based on the ‘Mirsini’ F1 variety from the Netherlands, had resistance to TSWV, which was confirmed by four markers: NCSw003, NCSw007, NCSw011, and NCSw012. Two cultivars, ‘Nicola’ and ‘Malinovyi Slon’ (Russia), and the local hybrid based on ‘Yarkiy Rumyanets’ had two to three resistant alleles of markers based on locus Tm-3 of resistance to TYLCV. The obtained results have demonstrated that the collection of tomato varieties involved in breeding programs in Kazakhstan lacks well-known genetic resistance factors to the considered tomato viruses. Thus, the prospective breeding programs require introduction of known resistant genetic resources to establish resistance to viruses using marker-assisted selection. Tomato; Tomato mosaic virus; Tomato spot wilt virus; Tomato yellow curl leaf virus; SCAR; CAPS.