This study investigates the micromorphological characteristics of pollen grains and leaf epidermal cells from 20 accessions across four species of spiny almonds using scanning electron microscopy. Thirteen quantitative traits of pollen grains, including exine sculpturing, were analyzed alongside qualitative features such as shape, exine sculpture type, and aperture type. Additionally, four quantitative and five qualitative features of the leaf epidermis were examined, focusing on cuticular ornamentation patterns, types of epicuticular wax, and stomatal measurements. The pollen grains were found to be isopolar monads, radially symmetric, medium‐sized, varying from prolate spheroidal to prolate, and exhibiting 3‐colporate to 3‐colpate structures. The exine sculpturing was generally striate with short and long ridges, with or without perforations, and could be classified into three types. Notably, in the Isfahan population of Prunus lycioides and the North Khorasan population of Prunus spinosissima, the exine sculpture types were distinctly different, being rugulate and reticulate, respectively. Multivariate statistical analysis identified equatorial diameter, colpus length and width, and ridge width as key diagnostic markers for species identification within spiny almonds. Principal component analysis and hierarchical clustering further highlighted the significance of stomatal length, cuticular ornamentation patterns, and epicuticular wax types in differentiating among taxa. We conclude that groupings recognized in recent classifications of the subgenus Amygdalus (spiny almonds) remain challenging to delineate solely based on palynological data, as diverse pollen types are present across different clades and subclades. Furthermore, micromorphological leaf traits proved valuable in distinguishing certain spiny almond taxa, and the traits of epidermal cells may reflect the ecological adaptations of spiny almond species.