Transcriptional regulation mediated by the balance of histone acetylation and deacetylation is fundamental in responding to environmental cues by impacting chromatin remodeling. Histone deacetylases (HDACs) are enzymes that remove acetyl groups from histone and non-histone proteins, thus restoring a tight chromatin structure. In pathogenic fungi, HDACs have been implicated in growth, secondary metabolite biosynthesis, and virulence. However, the role of HDACs in the mycotoxin fumonisin B1 (FB1)-producing fungus Fusarium verticillioides is poorly understood. In this study, we systematically characterized six F. verticillioides HDACs. An increased level of H4K16ac was observed in the deletion mutant of FvHOS2, which was associated with vegetative growth, conidiation, and virulence when infecting sugarcane and maize. FvRpd3 appeared to be essential for vegetative growth, while FvHda1 promoted growth, and both contributed to conidiation and pathogenicity. In contrast, FvSirt4 displayed a negative correlation with these processes. Additionally, the FB1 production was positively affected by FvHos2 and FvRpd3, but negatively impacted by Fvhda1, FvSir2, FvHst2, and FvSirt4 through the regulation of different key fumonisin biosynthetic (FUM) genes. Further findings indicate an association between FvSirt4 and FvSkb1, which is a histone methylase that positively regulates FB1 and pathogenicity. Moreover, as a global transcriptional regulator, over 2365 genes (~15% of the genome) enriched in multiple metabolic pathways were significantly downregulated in the ΔFvhos2 mutants relative to the wild type. Overall, our results suggest distinct roles of HDACs in regulating the growth, virulence, mycotoxin FB1 production, and gene expression in F. verticillioides.