Fusarium wilt in Chrysanthemums, a long-standing issue, is primarily caused by Fusarium equiseti, though confusion persists about its specific forma specialis. This study first identified and validated the pathogenic fungus in Chrysanthemum morifolium using Koch’s postulates. In response to the environmental impact of chemical pesticides, the study focused on biocontrol alternatives. Healthy C. morifolium rhizosphere soil was sampled to isolate antagonistic bacteria. Bacillus amyloliquefaciens, showing a 3.9 cm inhibition zone in plate confrontation tests, was identified as a potent biocontrol agent. Puncture inoculation tests on detached leaves and live plants demonstrated that lesion size in plants treated with both the pathogen and B. amyloliquefaciens was significantly reduced compared to controls, confirming the bacterium’s efficacy in inhibiting Fusarium wilt. This research provides a foundation for developing sustainable biocontrol methods for managing this disease in agriculture.