The distinctive features of floral nectaries facilitate identification of ecological and phylogenetic links between related taxa. The structure and functioning of nectaries determine the relationships between plants, pollinators, and the environment. The aim of the study was to determine and compare the micromorphology of the epidermis in the floral nectaries of six Rubus idaeus cultivars belonging to biennial (‘Glen Ample’, ‘Laszka’, ‘Radziejowa’) and repeated fruiting (‘Pokusa’, ‘Polana’, ‘Polka’) groups. Another objective was to characterize the cuticle ornamentation and stomatal morphology, the anatomy of the nectary epidermis, parenchyma, and sub-nectary parenchyma in the initial nectar secretion phase, as well as the ultrastructure of the nectary epidermis and parenchyma cells in the initial and full nectar secretion phases. The study was carried out using light, fluorescence, scanning and transmission-electron microscopy techniques. Semi-thin and ultrathin sections were used for the microscopic analyses. The cuticular ornamentation and stomatal morphology may be helpful elements in the identification of relatedness between Rubus species. The interaction of the extensive system of endoplasmic reticulum membranes, mitochondria, and Golgi apparatus indicates high metabolic activity, and the fusion of transport vesicles with the membrane suggests granulocrine nectar secretion. The results bring new data to the biology of plants.