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The study of microbes associated with the coffee tree has been gaining strength in recent years. In this work, we compared the leaf mycobiome of the traditional crop  Coffea arabica  with wild species  Coffea racemosa  and  Coffea stenophylla  using ITS sequencing for qualitative information and real-time PCR for quantitative information, seeking to relate the mycobiomes with the content of caffeine and chlorogenic acid in leaves.  Dothideomycetes ,  Wallemiomycetes , and  Tremellomycetes  are the dominant classes of fungi. The core leaf mycobiome among the three  Coffea  species is formed by  Hannaella ,  Cladosporium ,  Cryptococcus ,  Erythrobasidium,  and  Alternaria . A network analysis showed that  Phoma , an important  C. arabica  pathogen, is negatively related to six fungal species present in  C. racemosa  and  C. stenophylla  and absent in  C. arabica . Finally,  C. arabica  have more than 35 times the concentration of caffeine and 2.5 times the concentration of chlorogenic acid than  C. stenophylla  and  C. racemosa . The relationship between caffeine/chlorogenic acid content, the leaf mycobiome, and genotype pathogen resistance is discussed.

Differences between the Leaf Mycobiome of Coffea arabica and Wild Coffee Species and Their Modulation by Caffeine/Chlorogenic Acid Content