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This species is a tree of cloud forests with showy white to pink flowers and capsular woody fruits. This is the most commonly collected species of Cinchona as well as having the broadest geographical and ecological ranges. It is variable morphologically, and its separation from other Cinchona species has sometimes been difficult. Andersson (1998) clarified the taxonomy of this genus and noted, as discussed further in the notes for this genus, that many species of Cinchona including this one hybridize locally to produce populations that are difficult to assign to a particular species.
Cinchona pubescens is one of the main commercial sources of the antimalarial febrifuge quinine, which is found in commerically usefl quantities in its bark. Quinine is produced from cultivated trees not only of this species, but also of Cinchona calisaya and numerous hybrids between these and some other Cinchona species.