Most studies on Cinchona officinalis, the ‘quina tree’, have focused on its pharmaceutical properties, while agro-ecological aspects have received little attention to date. Studies about its association with arbuscular mycorrhizal fungi (AMF), which represent an important clade of beneficial soil fungi, are still scarce. Especially, the AMF partners of C. officinalis and their diversity has never been determined. These microorganisms play a crucial role in plant establishment across diverse ecosystems by enhancing water and nutrient uptake from the soil, suppressing root pathogens and pests, and contributing to overall plant health and resilience. The current study aimed at analyzing the arbuscular mycorrhizal root structures, at visualizing this mutualistic relationship between C. officinalis and AMF, and to identify the AMF species in the rhizosphere of the ‘quina tree’. Rhizosphere soil and roots were collected from a native population of C. officinalis in an Andean tropical forest in the Amazonas region, in Peru. Seventeen AMF species were isolated and morphologically identified. They belonged to eight genera (Acaulospora, Glomus, Funneliformis, Rhizoglomus, Septoglomus, Scutellospora, Sclerocystis and Ambispora) with highest diversity on species level among the AMF detected in Acaulospora. Roots of C. officinalis showed high AMF colonization (mean = 89%) in the form of different symbiotic structures, such as, vesicles, arbuscules and hyphae. By means of molecular analysis, we also detected rDNA of AMF in C. officinalis roots. Our results confirm the AMF association in C. officinalis with multiple species and a very high AMF root colonization under natural conditions, which opens opportunities for future research to screen the potential of this symbiosis to increase the sustainable productivity on this representative Peruvian tree.