Fusarium basal rot (FBR) caused by Fusarium oxysporum is one of the most destructive diseases of shallot in Vĩnh Châu, Sóc Trăng. This study aims at testing for the effects of aqueous leaf extracts of Annona glabra and Wedelia calendulacea on FBR under greenhouse and storage conditions to bio-control this disease. Under greenhouse conditions where shallots were inoculated with F. oxysporum before planting, the 5% (w/v) extracts of A. glabra and W. calendulacea significantly reduced the disease incidence (up to 61% and 59%, respectively) and severity (up to 63% and 61%, respectively) at all assessment time points (37, 44, 51, 58 and 65 days after planting). Under storage conditions, all extract treatments exhibited disease-reducing effects at all time points (7, 14, 21, 28 and 35 days after pathogen inoculation). The 5% extracts of A. glabra and W. calendulacea showed highest bio-control efficacy, reducing disease incidence up to 68% and 66%, respectively. Thus, A. glabra and W. calendulacea showed their potentials for large-scale applications to bio-control FBR of shallot.