This species as recognized by Andersson (1998) includes shrubs and small trees found naturally in mountain forests of a rather small region of the Andes of southern Ecuador. As with many Cinchona species, the separation of C. officinalis has sometimes been problematic due to morphological variation, local hybridization, and confusion over the separation and identification of species. Andersson clarified the separation of this species, in particular from C. calisaya, which is a similar species that is widely cultivated species as one of the commercial sources of quinine. Because of the confusion of these two species, many authors have used the name C. officinalis for the cultivated plants, and thus many of the photos, specimens, and ecological and chemical studies of "C. officinalis" actually treat misidentified plants of C. calisaya. It appears that C. officinalis contains no commercially useful quantities of quinine in its bark and has been cultivated only occasionally (Andersson, 1998).

Cinchona officinalis can be recognized within its genus by its leaves that are generally rather acute at the apex and have the domatia predominantly found in the basal (proximal) portion, its calyx limb quite deeply lobed, and its fruits with fairly thick-textured walls; vs. the leaves mostly obtuse to rounded at the apex and with the domatia mostly found in the upper (distal) portion, its calyx limb shallowly lobed, and its fruits with rather papery walls in C. calisaya. Cinchona officinalis is one of only a few species of this genus that Andersson diagnosed as always having pit domatia on the leaves, vs. variable in this regard.