【Objective】As a serious banana disease and a significant limiting factor in banana production worldwide, banana Fusarium wilt disease is caused by the fungal pathogen Fusarium oxysporum f. sp. cubense race 4(FOC). The rhizosphere microbiome of plants is a key barrier that defends plant roots from an invasion of soil-borne pathogens. Most studies of the rhizosphere microbiome have focused on bacterial and fungal communities. However, as an important component of the rhizosphere microbiome, the rhizosphere protist community has been neglected in the regulation of microbiome and plant health. This study was conducted to explore the characteristics of the soil protist community in healthy and diseased plants and the interactions between protists and pathogens through field experiments of continuous cropping of bananas.【Method】In this paper, high-throughput Illumina MiSeq sequencing was applied to analyze the differences of soil protist community structure and composition among different treatments in field experiments.【Result】Results show that the relative importance of protists in predicting pathogenic Fusarium number was 47.19%, suggesting that protists might be the best predictor for pathogen number than culturable bacteria and fungi. The diversity and richness of the rhizosphere protist community decreased during plant growth and was lower in diseased plants. The composition and community structure of protists differed between healthy and diseased plants in rhizosphere soil. Also, the relative abundance of phagotrophic protists was highest compared to other functional groups in all soil samples, showing an increasing trend throughout plant development and enriched in diseased plants. Before the heading stage, the relative abundance of Bacillariophyta_X_unclassified, a phototrophic protist, was highest in healthy plants but decreased at a later stage. In healthy plants, the relative abundances of Group-Te and Cercomonas, phagotrophic protists, were higher at the heading stage. It was also observed that diseased plants showed a higher relative abundance of Pythium while phagotrophic protists, particularly Cercozoa protists, had significant correlations with Fusarium than other protistan communities. Group-Te and Cercomonas, two Cercozoa taxa, were negatively linked with the pathogen. In contrast, pathogens in diseased plants were positively linked with Pythium, which was a plant pathogenic protist. 【Conclusion】Protists in the rhizosphere soil demonstrated a greater impact on pathogens. The community characteristics of protists in rhizosphere soil changed in the process of plant growth and differed between healthy and diseased plants. Particularly Group-Te and Cercomonas were negatively linked with the pathogen, which might have potential in the prevention and control of banana wilt disease. Future research should focus on(i)the isolation and purification of phagotrophic protists negatively related to pathogens, (ii)exploring the mechanism of phagotrophic protists and pathogens, and(iii)investigating the internal connection with other beneficial microorganisms in rhizosphere soil to improve the efficiency of controlling banana wilt.