Walnut (Juglans regia L.) is a monoecious species and although it exhibits self-compatibility, presents incomplete overlap of pollen shed and female receptivity. Thus, cross-pollination is prerequisite for optimal fruit production. Cross-pollination can occur naturally by the wind, the insects, artificially, or by hand. Pollen has been recognized as one possible pathway for Xanthomonas arboricola pv. juglandis infection, a pathogenic bacterium responsible for walnut blight disease. Other than the well-known cultural and chemical control practices, artificial pollination technologies with the use of drones could be a successful tool for walnut blight disease management of orchards. Drones may carry pollen and release it over crops or mimic the action of bees or other pollinators. Although this new pollination technology could be regarded as a promising tool, pollen germination and knowledge of pollen as a possible pathway for the dissemination of bacterial diseases remain crucial information for design and manufacture of aerial pollinator robot for walnut trees. Thus, our purpose was to describe a pollination model with fundamental components, the identification of the “core” pollen microbiota, specify an appropriate flower pollination algorithm, design an autonomous precision pollination robot, and minimize the average errors of flower pollination algorithm parameters through machine learning and meta-heuristic algorithms.