The insufficient pollinator visitation is the most important limitation of fruit and seed production, which is common and ubiquitous in entomophilous angiosperms. The scent and attractive colours with flower guides and such floral rewards as nectar, pollen, and oil are important attractants for insects visiting and pollinating flowers in the family Iridaceae. The aim of this study was to investigate the morphology of flowers and the micromorphology, anatomy, and ultrastructure of floral nectaries in the rare and endangered species Iris sibirica with the use of light, scanning, and transmission electron microscopes and histochemical assays. Osmophores in the form of papillae were located on the adaxial surface of outer tepals and on the abaxial surface of the stylodium channel. The nectaries were located on the inner surface of the perianth tube and were composed of a single-layered epidermis with papillae and several layers of glandular parenchyma with vascular bundles. I. sibirica nectaries represent the presecretory starch-accumulating type, where nectar is released for a short time immediately after flower opening. Nectar was produced throughout the flower lifespan in both male and female stages. It was secreted in the granulocrine mode and released through microchannels in the reticulate cuticle of nectary papillae. Transport of pre-nectar components proceeded via symplastic and apoplastic pathways. The nectary epidermal cells with papillae and glandular parenchyma cells contained total lipids, acidic lipids, and polysaccharides, whereas the epidermal cells with papillae additionally contained neutral lipids and polyphenol compounds. The nectaries and nectar production in I. sibirica flowers share the common location and follow several secretion patterns characteristic for the nectaries in some members of the family Iridaceae and the subfamily Iridoideae. Nevertheless, the mode of nectar release through the cuticle of epidermal papillae has been described in Iridaceae family for the first time. The visual, aromatic, and food attractants characteristic of I. sibirica flowers probably stimulate potential visits by pollinators, but the short nectar secretion period may limit the effectiveness of pollinators and sexual reproductive success.