Species composition, quantitative indicators and the occurrence of bacteria and fungi associated with apple shoots in the Saratov region were studied. On the surface shoots isolated 12 species of bacteria, and 4 species of fungi, of the internal environment – 14 species of bacteria and 3 species of fungi. The most common surface associates apple shoots appeared bacterium Bacillus subtilis, Pantoea agglomerans, fungus Alternaria sp. and Fusarium tricinctum, internal environment shoots – Bacillus subtilis, Bacillus amyloliquefaciens, Penicillium sp.