The ectomycorrhizal (EcM) roots of Cedrus deodara associated with a unique hypogeous EcM fungus—Rhizopogon himalayensis is meticulously characterized and comprehensively described based on well‐established standard morphological and anatomical features. The mycobiont—R. himalayensis was found organically associated with the roots of C. deodara. The EcM morphotypes are distinguished by differences in the shape and color of the roots, type of ramification, surface texture, type of mantle, as well as different chemical reactions. All the examined morphotypes were having similar mycorrhizal system and anatomically (Mantle and Hartig net) no disparities were seen, that is, nonsignificant (p > 0.05) variations were observed. The majority of mycorrhizal systems were irregularly pinnate, dichotomous type with 0–1 order of ramification and occasional coralloid type. Mantle surface was densely cottony to loosely wooly. The outer and inner mantles were H & Q type. Hartig net was a complex net‐like structure with uniseriate to mutiseriate type of hyphal cell arrangement. Rhizomorph were smooth and round, consistently growing along roots. Moreover, extraradical hyphae were hyaline, septate, and without clamp connections. Sclerotia and cystidia were absent. Our findings will contribute to the biology of ectomycorrhizae associated with primitive and economically valuable conifers, thriving in the face of shifting environmental conditions in the northwestern Himalayas.