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<i>Allium</i> species are known for their culinary, medicinal, and ornamental purposes. Fusarium basal rot is one of the most damaging soilborne fungal diseases of <i>Allium</i> species and poses a significant threat to yield, quality, and storage life worldwide. Various species of <i>Fusarium</i> have been identified as causal agents for Fusarium basal rot, depending on the <i>Allium</i> species involved. Diverse disease management practices have been implemented to mitigate the impact of Fusarium basal rot. This review article provides a comprehensive overview of the recent progress in detecting different species of <i>Fusarium</i> involved in Fusarium basal rot and strategies to control them in affected <i>Allium</i> species involving chemical, biological, and cultural methods. It covers the latest advancements in host plant resistance research from traditional breeding to modern molecular techniques and studying secondary metabolites involved in defense mechanisms against Fusarium basal rot.