Fusarium wilt and other soil-borne vascular diseases remain major constraints to sustainable crop production because their causal agents persist in soil, interact intimately with host roots, and are difficult to eradicate using conventional management practices. Increasing concerns regarding pesticide residues, environmental contamination, pathogen resistance, and deterioration of soil biological health have stimulated interest in rhizosphere-based biological control. Rhizospheric fungi, particularly Trichoderma, Clonostachys, arbuscular mycorrhizal fungi, selected Penicillium spp., and non-pathogenic Fusarium isolates, can suppress soil-borne pathogens through complementary mechanisms including mycoparasitism, competition, antibiosis, hydrolytic enzymes, volatile organic compounds, nutrient mobilization, root colonization, induced systemic resistance, hormonal modulation, and restructuring of the soil microbiome. Recent research indicates that disease suppression should increasingly be viewed as an emergent property of the plant–pathogen–microbiome–environment continuum rather than as the consequence of direct antagonism by a single microorganism. Disease-suppressive soils, microbiome engineering, synthetic microbial communities, multi-omics, precision formulation, and controlled delivery are consequently emerging as important directions for next-generation biocontrol. Recent studies further demonstrate that root exudates and agricultural practices can reshape rhizosphere communities associated with Fusarium suppression, while advances in formulation technology are improving the stability and applicability of fungal inoculants. Beyond terrestrial agriculture, fungal biotechnology offers an emerging connection with agro-aquaculture through nutrient recycling, agricultural-residue valorization, wastewater treatment, fungal–microalgal systems, and circular bioeconomy approaches. However, direct introduction of terrestrial fungal biocontrol agents into aquatic production systems remains premature and requires independent ecological, toxicological, and regulatory assessment. This review critically synthesizes the ecology, mechanisms, biotechnology, formulation, field constraints, climate-resilience potential, and agro-aquaculture prospects of rhizospheric fungi, and proposes a systems-level framework for their integration into sustainable disease management.
