Self-fertility is an economically valuable trait, which allows the genetic diversity of plants in the natural environment to be maintained. The key mechanisms underlying this phenomenon have been extensively studied by the methods of breeding and genetics. However, there is a lack of knowledge in the fi eld of biochemistry concerning the eff ects of various chemical substances on the self-fertility of plants. Although there exist hypotheses about the role of fl avonoids in pollination, their infl uence on the mechanism of self-incompatibility remains unclear for many crops. In this research, we analyse the spectral characteristics of pistil extracts from cultivars of domestic plum (Prunus domestica L.) and common cherry (Prunus cerasus L.), which diff er in self-fertility, and evaluate the content of fl avonoids in pollen. The results showed diff erences in the content of chemical substances between self-fertile and self-incompatible varieties of cherry and plum, which can be further used to study self-compatibility factors in these crops. Future studies will analyze the substances contained in reproductive organs by high-performance liquid chromatography (HPLC) to determine the self-fertility factor of domestic plum and common cherry.