The plant-associated microorganisms are of key importance in ensuring the quality and safety of plant products. This paper focuses on the study and composition of endophytic microorganisms inautumn apple varieties from domestic selection intended for long-term storage: Bessemyanka Barantseva, Orlovsky Pioner, Alesya and Verbnoe.It was discovered that the internal tissues of fruits are richly populated with microorganisms, the number of which depends on the plant variety and the stage of fruit development. The dominant group is yeast (up to 107 CFU/g). The most common speciesis Hanseniaspora uvarum (26,0%). The number of bacteria averages 102-104 CFU/g, the dominant species–Lactobacillus sp. (52,0%) and Pantoea agglomerans(34,2%). The soft tissue of the fruits of all studied apple varieties contains mycelial fungi, the number of which, as a rule, does not exceed 102 CFU/g. The dominant species is Cladosporium aggregatocicatricatum (33,3%). The microorganisms - producers of biologically active compounds, promising for agrobiotechnologies, have been identified.