The cherry fruit yield in Chilean orchards is subject to variability year to year, which needs to be studied in order to stabilize and increase production and economic results. During flowering and fertilization, many flowers do not set, attributing generally climatic causes or floral overlap problems in auto-incompatible cultivars. The aim of this study was to assess microscopic methods to follow the flowering process and fruit set that allowed discriminating factors causing poor fertilization. For this, during the 2011 season in La Palma Experimental Station of Pontifical Catholic University of Valparaiso, we worked with 'Brooks' and 'Lapins'/MaxMa14 trees characterizing flower buds in 2-year-old branches, in different stages. Pollen was analyzed and monitored by fluorescence microscopy to the set process. In the dormant stage, pistils and stamens of both varieties were completely differentiated; the ovules were in early stages of differentiation, however, the pollen did not initiate this process yet. In both cultivars starch was not detected until starting green tip, where it was observed in anthers, style, ovules and ovaries, indicating that starch is detectable when the buds start scales opening and exposure of flower primordia. The pollen quality of all pollinator cultivars was good and for all observations it was possible to visualize its presence in the stigmatic surface. The migration of pollen tubes in the style and ovarian cavity, achieved a higher growth rate in 'Lapins', where it was possible to observe set from 72 h after the balloon stage, while in 'Brooks' it was scarce until 120 h.