The selection of the cereal crops varieties as a factor in the regulation of the phytopathogenic microbiome in agrocenoses is an actual direction of the research. Cultivation of such varieties leads to a decrease in the level of biological pollution in agrocenoses and increases the quality and safety of agricultural products in agroecosystems. Therefore, the influence of the environmental factors (including abiotic, biotic, anthropogenic, and other ones) on the formation of micromycete populations in the leaf microbiome of grain crops using different plant cultivation technologies has been thoroughly studied earlier. The results of the selection the plant varieties by the indicators of influence on their population density, the frequency of the occurrence, and the intensity of the micromycete sporulation, are presented in this article. Vegetative organs of plants of the cereal crops (including the oats of Parliamentsky variety, Tembre variety, and spring barley Salomi and Sebastian varieties) were selected in the following phases: tillering, stem stage of growth, and earing. It was determined that using the traditional and organic technologies of plant cultivation in the leaf microbiome of Tembre oats and Salomi variety spring barley, the population density, the frequency of the occurrence of micromycete species, and their sporulation intensity were significantly lower compared to the plants of Parliamentsky oat and Sebastian spring barley. This shows that the cultivation of the cereal crops varieties capable of restraining the formation of micromycete on an ecologically safe level will result in a decrease in the level of biological pollution of agrocenoses and increase the biosafety of plants.