In this study, two species belonging to the genus Allium and distributed in Turkey are investigated. A thick cuticle is observed on the epidermis of the scapes of the species. The epicuticular layer is not evident in Allium scorodoprasum ssp. rotundum (L.) Stearn. Secretory cavities have been formed in the pith region of the species. Vascular bundles are in the form of two rings, one above and one below the sclerenchymatic ring. The cross- section of the leaf of Allium brevicaule Boiss. & Balansa is circular, unlike A. scorodoprasum ssp. rotundum. In both species, the stomata are located lower than the epidermis cells. The seeds of A. brevicaule are smaller than in A. scorodoprasum ssp. rotundum and they are polygonal shaped. The testa cells of A. brevicaule seeds have scalariform and tuberculate ornamentation. A. scorodoprasum seeds have reticulate sculpture testa. The species have sulcate pollen types. The pollen form of A. brevicaule is perprolate, and that of A. scorodoprasum ssp. rotundum is subprolate. The apertures in both species are monosulcus. In A. brevicaule, the sulcus does not extend to the poles at the proximal end. Therefore, the differences in the scape and leaf anatomy, as well as in palynology and micromorphology, can be used to distinguish Allium species.