Allium (Amaryllidaceae) is diverse and taxonomically problematic, with controversial subdivisions and polymorphic species. In Egypt, the genus has not been investigated satisfactorily in terms of palynology. The present study aims to provide palynological information on the endemic and near-endemic species of Allium for the first time in Egypt and to characterise the pollen diversity of the investigated taxa. The pollen morphology of 21 Allium taxa was studied comprehensively via Scanning Electron Microscopy. Twenty-five traits were surveyed, then subjected to hierarchical cluster analysis (HCA) and principal coordinate analysis (PCoA). Pollen grains are monads, heteropolar, monosulcate, or trisulcate, small to medium-sized (polar axis (P) = 10.44–29.76 μm, equatorial diameter (E) = 18.97–59.24 μm), and peroblate or oblate in shape. The sulcus may be anasulcate, meridionosulcate, or subzonasulcate. Sulcus ends are blunt, pointed, rounded, or undulated. The exine ornamentation is variable and diversified between the distal pole and the equator. The current study highlights the importance of pollen characteristics such as pollen size parameters, pollen shape, aperture type, polar outline, sulcus size parameters, sulcus type and end shape, distance between sulcus ends, exine ornamentation, presence or absence of perforations on the exine, and perforation size and density for the discrimination of Allium taxa in Egypt. The HCA confirms that pollen morphology has limited taxonomic usefulness at the sectional level for the studied taxa. The PCoA results, on the other hand, were more informative to visualise the infrageneric classification based on the studied palynological traits. A dichotomous identification key for 21 Allium taxa in Egypt based on palynological data is presented.