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Adix pseudostellariae is a perennial herb with significant medical potential that is used as a tonic. Production and quality suffer significantly when this plant is repeatedly monocultured in the same field. In this work, a 3-year field experiment was conducted to determine the growth inhibitory effect brought on by R. pseudostellariae's protracted monoculture. Along a 3-year monoculture gradient, DGGE analysis was utilised to investigate changes in the composition and diversity of soil Fusarium and Pseudomonas populations. The findings showed that prolonged monoculture considerably increased the diversity of Fusarium species while decreasing the variety of Pseudomonas species. Although Pseudomonas spp. experienced a reduction, quantitative PCR analysis revealed a considerable increase in Fusarium oxysporum. Furthermore, the abundance of hostile Pseudomonas spp. with antagonistic potential against F. oxysporum decreased significantly in successively monocultured soils.While inhibiting the growth of antagonistic Pseudomonas sp. CJ313, a phenolic acid mixture at the same ratio as that found in soil could promote the mycelial and sporular growth of pathogenic F. oxysporum. Additionally, Pseudomonas sp. CJ313 performed well in plant bioassays, preventing F. oxysporum from infecting R. pseudostellariae. In conclusion, this study showed that Fusarium and Pseudomonas populations in the plant rhizosphere might be altered by an extended monoculture of R. pseudostellariae, resulting in a relatively low level of antagonistic microorganisms but a comparatively high level of pathogenic bacteria.