To understand the diversity of the rhizosphere soil microbial and endophytic fungi from the typical karst species-A. luodianensis, rhizosphere soil and healthy plants were collected through Isometric sampling method, then the soil microbial and endophytic fungi were isolated by culturable cultivation, and identified using the molecular technology. Finally, we constructed a phylogenetic tree, and calculated the diversity index according to the results, which reveal the conclusion:(1)Totally, there are 139 fungal isolates was obtained from rhizosphere soil, root, stem and leaf, belonging to 27 genera. Among them, 34 fungi strains were isolated from rhizosphere soil, belonging to 12 genera; 63 endophytic fungi strains were isolated from the roots, belonging to 17 genera; 14 endophytic fungi strains were isolated from the stems, belonging to 8 genera, 28 endophytic fungi strains were isolated from the leaves, belong to 9 genera. (2)There are 41 bacteria strains were isolated from rhizosphere soil, belonging to 7 genera and 26 species totally; 20 actinomycetes strains, belonging to 1 genus and 15 species. According to the order of microorganism diversity index, there was a significant difference in fungal diversity:root > rhizosphere soil > stem > leaf, but it was not significant in the diversity of bacteria and actinomycetes. (3)Fungi, bacteria and actinomycetes were divided into 3 branches by hierarchical cluster analysis. We found that the microbial diversity in rhizosphere soil, root, stem and leaf of A. luodianensis was abundant, and there was a significant difference in microbial community composition in different parts (P < 0.05), salt-tolerant and drought-tolerant bacteria groups with pseudomonas and bacillus were the dominant genera here. This study laid a foundation for searching for functional bacteria related to A. luodianensis, which would help to reveal the adaptability of A. luodianensis to karst habitat and provide some basic data for the relationship between microorganism and plant community.