The genus Capparis L. (Capparaceae) comprises edible plants and species with medicinal properties. Capparis spinosa is widely distributed in Europe, Africa, Asia and Oceania. This taxon forms a polymorphic species complex within that, several species and infraspecific taxa have been identified. We have focused on the leaf anatomy and micromorphology of Capparis taxa in Iran to find efficient diagnostic characters. Fresh samples of different taxa studied of C. spinosa were collected. Leaf-blade cross-sections and leaf surface were considered. Multivariate statistical analyses were used for illustrating the species and varieties similarities. Leaf anatomical features, such as midrib vascular bundle width and length, abaxial and adaxial epidermis thickness, abaxial and adaxial cuticle thickness, stomata depth, midrib outline on the adaxial surface, epicuticular wax, stomata average length, stomata number per leaf area and trichome type on the leaf surface were of diagnostic importance. As there is some degree of taxonomic confusion between different varieties of C. spinosa and mainly herbarium samples can provide stems and leaves for analyses, our anatomical study tries to overcome this problem. Results showed that selected features are of taxonomic importance in species and varieties separation.