The paper provides data on the use of the Malus sieboldii Rehd. as a genetic donor of economically valuable traits in breeding low-vigorous clonal apple rootstocks. The method of embryo culture is proposed as a way to increase the efficiency of distant crosses. The studies were carried out using seeds obtained in three combinations of crossing (M. sieboldii x Malysh Budagovskogo, M. sieboldii x 60-160, M. sieboldii x 76-3-6). As sterilizing agents when introduced into culture in vitro, we used industrial disinfectant «Belizna (Whiteness)», the sanitizer «Ecocid C» + «Belizna» and the sanitizer «BioPag C» + «Belizna». It was found that additional pretreatment with «Ecocid C» (1.0%) and "BioPag C" (0.4%) for 50 minutes before using the disinfectant «Belizna» contributes to the production of sterile explants up to 61.5% compared to the control. The best results were obtained when combine using «Ecocid C» (1.0%, 50 min.) and «Belizna» (50%, 5 min.). After 28 days, due to the low number of developing embryos, the method of dissection of a part of the cotyledons of hybrid seeds was used. As a result, up to 65.3% of hybrid plants were obtained, compared to 4.2% of the control.