Phytoplasma diseases of seed crops are of economic importance, both in foreign countries and on the territory of the Russian Federation. One of the harmful phytopathogens are phytoplasmas Candidatus Phytoplasma mali (causative agent of apple proliferation) and Candidatus Phytoplasma pyri (causative agent of pear depletion). The spread of phytoplasmas is carried out with the help of psyllas and leafhoppers, infected planting material, and parasitic plants. Symptoms of infection with these phytopathogens are branching shoots, small leaves with enlarged stipules, yellow or orange shade of leaves, necrosis. Phytoplasma infection may be in a latent state without symptoms. Diagnostics of phytoplasmas using molecular genetic diagnostic methods will allow the use of measures to limit the spread of harmful microorganisms. This paper presents part of the research on the diagnostics of pathogens of apple proliferation and pear depletion, according to International Protocols for the diagnostics of harmful organisms. Universal primers and a probe for the detection of Candidatus Phytoplasma mali and Candidatus Phytoplasma pyri using domestic reagents have been tested. The research was conducted on the basis of All-Russian Centre of Plant Quarantine (FSBI “VNIIKR”) together with colleagues from LLC “RPC Syntol” and FSEI HE RUDN.