The aim of this study was to assess and compare the pharmacognostic and microscopic features of the selected parts of Rhododendron afghanicum Aitch. & Hemsl. It is a perennial and shrub. Anatomy of stem and leaves depicted dicot structure. It will provide knowledge about standardization, authentication, and adulteration with its co-species. The macroscopic examination reveals that fresh leaves are green, pleasant odor with a bitter taste. The leaf is oblong-elliptic in shape and sub-acute at apex; rounded at the base with entire margin. Stem is irregular and the outer surface is light brown, rough with fissures and ridges. Microscopic examination indicated the presence of xylem, phloem, peltate trichome, epidermal cells, collenchymas cells, paracytic stomata, and reticulate vessels. Stem microscopy reveals epidermis, hypodermis, cortex, sclerenchymatous sheath, phloem, xylem, and pith. It will be helpful in identification and quality control. Micro-morphological features were observed through SEM. EDX spectroscopy were carried out and revealed the presence of calcium, silicon, and potassium. Phytochemical analysis revealed the presence of tannins, saponins, phenols, protein, flavonoids, glycosides, and alkaloids. Ethyl acetate for leaf and stem demonstrate the highest extractive values (18% and 13%), respectively. XRD peaks appeared at 30.21, 28.73, 205.73, 200.73, 380.07, 390.24, 490.11, and 450.33ο . This will be helpful to identify the ownership of herbal drugs by the diffraction peaks through crystal structures and atomic spacing. These parameters are crucial for drug identification, standardization, authentication, and drug designing. These studies also provided knowledge regarding therapeutic and nutraceutical importance of this plant. RESEARCH HIGHLIGHTS: The current pharmacognostic studies carried out on Rhododendron afghanicum can serve as a basis for compiling keys for finding the taxonomic identification and authentication of the said species by morphological, anatomical, and physicochemical features.