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[Objective J The present paper aimed to explore the diversity and distribution rules of soil microbial community of Annona squamosa Lour. after the infection of root rot, and provide a reference basis for the screening and identification with A. squamosa pathogens of root rot. [Method J Samples of A. squamosa rhizosphere soil infected with root rot (infected rhizosphere soil) and healthy rhizosphere soil (healthy rhizosphere soil) were collected. Using high throughput sequencing technology and designing primers of ITSl and 1154,sequenced the fungal ITSl and bacterial V3 + V4 regions, and analyzed the structure and diversity of the phylum, class, order, genus, and species level. [Result] After infection with root rot, the number of fungi in its rhizosphere soil increased greatly, and the number of bacteria decreased. The classification of fungi in rhizosphere soil belonged to 2 kingdoms,5 phylum, 16 classes,36 orders,48 families,81 genera and 96 species. The classification of fungi of healthy rhizome soil belonged to 3 kingdoms, 7 phylum, 17 classes, 43 orders, 73 families, 113 genera and 160 species. The community richness and diversity index of the rhizosphere soil microorganisms decreased compared with healthy rhizosphere soil, along with fewer types of soil fungi, and uniform distribution of soil fungi. After 4 days, medium and radioactive strains were formed on PDA medium; the strains formed medium, radioactive gas bacteria; colony diameter 4. 5 cm, bacteria flat spread, full edge, round, white, gas bacteria velvet. Rhizosphere soil pathogen strains were amplified using trial primers, the results showed that the displayed strain ITS sequence and Fusarium acutatum (accession number: AY569567. 1) had 99. 45% homology, indicating the amplified ITS segment sequence (RRD- 1) was parts of F. acutatum sequences. [Conclusion] The community richness and diversity index of root soil microorganisms decreased greatly compared with that of healthy soil, and the types of soil fungi in pathogenic plants were less, and the uniformity increased. After pathogen morphological observation and biological comparison, the pathogen that caused root rot of A. squanwsa in Guangxi might be F. acutatum. [ABSTRACT FROM AUTHOR]