Rosaceae fruit trees are characterized by gametophytic self-incompatibility, with their production typically requiring artificial pollination or pollination tree is required in production. Both of these solutions cause reductions in production efficiency, and self-incompatibility has become a major issue in agricultural biology, and as such, has been extensively studied. In this review, we discuss the relationship between S-RNase content in the style and self-incompatibility, and the role of the SLF gene in stamen-determining factor. Considering mutations in self-compatibility-related genes and self-compatibility in polyploid fruit trees, we discuss the potential mechanisms of self-incompatibility. Based on a preliminary study of the role of pollen tube Ca2+ gradients in self-incompatibility in Pyrus, we propose a new mechanistic model of self-incompatibility taking into account the effect of Ca2+. We also discuss the potential for hormone regulation to be used to control self-incompatibility in Rosaceae fruit trees.