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BBX genes play an important role in plant growth, development, and stress response. However, systematic analysis of BBX gene family regarding resistance to fungal infections has not been previously conducted in Chrysanthemum. In this study, a systematic analysis of the BBX gene family was performed, and its function in defense of necrotrophic fungus Alternaria sp. has been probed into through publicly available genome and RNA-seq data of Chrysanthemum after Alternaria sp. infection. The systematic analyses included identifying the BBX gene family in Chrysanthemum, their evolutionary relationships, conserved domains, motifs, gene structure, cis -acting elements, and collinearity. Based on the RNA-seq data analyses and expressional pattern, CmBBX32 was selected as a candidate gene for further investigation because it responded continuously to the infection and up-regulated expression when Chrysanthemum was inoculated with Alternaria sp. Gene expression analysis showed the expression of CmBBX32 increased sharply during the infection process, and was highest in flowers. Besides, virus-induced gene silencing (VIGS) of CmBBX32 in Chrysanthemum reduced the resistance to Alternaria sp. infection, as evidenced by phenotypic analysis of infection symptoms, microscopic examination of spore germination and hyphal growth, as well as quantitative analysis of the marker gene associated with the SA and JA defense pathways. Overall, the data generated in this study should form the basis for future functional characterizations of BBX genes in Chrysanthemum, especially regarding the resistance to biological stress in Chrysanthemum.