Cordia diffusa K.C. Jacob, known as Sirunaruvili, belonging to the family Boraginaceae, is a rare endemic species. The study aimed to document the morpho‐anatomical and histochemical characteristics of C. diffusa to facilitate its identification, as it is a highly threatened steno‐endemic plant. The plant is an evergreen, woody shrub with brownish‐gray, lenticellate stems and oblong‐oblanceolate with pubescent leaves. Flowers are yellowish‐white, tubular, fragrant, and arranged in umbellate cyme. Fruits and drupe, turning from green to orange when ripe, with viscid edible pulp. Flowering and fruiting occur year‐round. The anatomical results showed that the adaxial surface of leaves had more stomata than the abaxial leaf surface. The pubescent plant surface was due to unicellular trichomes in the leaf's epidermal layer, and some of the epidermal cells had cystoliths. Petioles and stems had ridges, unicellular trichomes, and collateral vascular bundles with prominent water storage cells. Root exhibited radial vascular arrangements, cortical region, endodermis, and exarch xylem, with secondary growth forming periderm layers. Sclerenchymatous fibers and lignin accumulation were observed in the stem and roots. The histochemical study showed the presence of carbohydrates, proteins, lipids, acidic and neutral lipids, phenolic compounds, lignified cell walls, and alkaloids in various regions of the plant cell. The micro‐morphological properties of the plant exhibited several unique aspects for accurate taxonomic identification and species delimitation, and this work offers many valuable details to plant taxonomists for future research.