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Background  This study examined how rhizosphere fungi influence the accumulation of chemical components in fruits of a small population species of  Cinnamomum migao .    Results  Ascomycota and Basidiomycota were dominant in the rhizosphere fungal community of  C. migao .  Pestalotiopsis  and  Gibellulopsis  were associated with α-Terpineol and sabinene content, and  Gibellulopsis  was associated with crude fat and carbohydrate content. There were significant differences in rhizosphere fungal populations between watersheds, and there was no obvious change between fruiting periods.  Gibberella, Ilyonectria ,  Micropsalliota , and  Geminibasidium  promoted sabinene accumulation, and  Clitocybula  promoted α-Terpineol accumulation.    Conclusion  The climate-related differentiation of rhizosphere fungal communities in watershed areas is the main driver of the chemical composition of  C. migao  fruit. The control of the production of biologically active compounds by the rhizosphere fungal community provides new opportunities to increase the industrial and medicinal value of the fruit of  C. migao .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-021-02216-z.

Effects of rhizosphere fungi on the chemical composition of fruits of the medicinal plant Cinnamomum migao endemic to southwestern China