Abstract: 【Objective】 To analyze and compare structure and similar-to-host antimicrobial function of endophytic fungal microbiome in wild and cultivated Sophora tonkinensis Gagnep., and to provide reference for quality improvement of host medicine cultivation using beneficial endophytic fungal microbiome.【Method】 Endophytic fungi were isolated from roots of wild and cultivated S. tonkinensis by tissue block method, and then were identified based on morphological and ITS sequence characteristics;through agar block method and plate confrontation, with human pathogens and filamentous pathogenic fungi as the target bacteria, inhibition zone and inhibition rate of taxa of endophytic fungal microbiome in S. tonkinensis roots were determined, respectively.【Result】 Endophytic fungi of 234 strains of 36 taxa, and 48 strains of 10 taxa, were respectively isolated and identified from wild and cultivated S. tonkinensis roots. The numbers of genera, dominant genera, endemic genera, species and endemic species of endophytic fungal microbiomes in wild S. tonkinensis roots were 3-5 times of those in cultivated type, with α diversity index of endophytic fungal microbiome in wild S. tonkinensis roots significantly higher than that in cultivated type(P<0.05) and β-diversity index was very low between the two. The number of similar-to-host antimicrobial activity taxa of endophytic fungal microbiome in wild S. tonkinensis roots was 6-10 times of that in cultivated S. tonkinensis roots. Diameters of the inhibition zone of taxon Colletotrichum simmondsii against 3 human pathogens were equal to or greater than those of positive control. Nine taxa, Aspergillu. flavus, Phoma sp., Purpureocillium lilacinum, Trichoderma asperellum, Trichoderma sp., Talaromyces funiculosus, Fomitopsis sp., Fusarium solani and Rhexocercosporidium sp., showed inhibition rates higher than 50% against 3 filamentous pathogenic fungi.【Conclusion】 Endophytic fungal microbiome in wild S. tonkinensis root has habitat specificity, higher biodiversity, and strong broad-spectrum similar-to-host antimicrobial function, which will be beneficial to synthesize metabolites with unique structure, diverse bioactivity, so as to develop special effects in host medicine, thus improving cultivated medicine quality.