Breeding renewal of the southern assortment of apple trees for the Russian fruit growing industry based on the accelerated process of creating domestic genotypes with a complex increased resistance to the main fungal pathogens of the culture (Venturia inaequalis (Cooke) Wint., Podosphaera leucotricha (Ell. & Ev.) E.S. Salmon, Phyllosticta mali Pr. et. Del., Phyllosticta briardi Sacc.) is due to the systematic use of modern methods, innovative breeding techniques and improved techniques. The purpose of the study is to develop and create a database of representatives of the genus Malus Mill., which is promising for use in the production and accelerated breeding of new domestic genetic resources for the southern region of Russia. During the research work, Russian modern and generally accepted programs and methods of breeding, variety study for fruit plants were used. The formed database “Main economically valuable, morphological and molecular-genetic characters of representatives of the genus Malus Mill. with resistance to the main fungal pathogens in the south of Russia”; filed an application for its patent. Using the data of the obtained information system will significantly speed up the solution of practical selection problems and reduce the costs of organizing the breeding process.