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Fusarium ear rot, caused by Fusarium verti-cillioides, is a devastating fungal disease in maize that re-duces yield and quality; moreover, F. verticillioides pro-duces fumonisin mycotoxins, which pose serious threats to human and animal health. Here, we performed a genome-wide association study (GWAS) under three en-vironmental conditions and identified 34 single-nucleotide polymorphisms (SNPs) that were significantly associated with Fusarium ear rot resistance. With reference to the maize B73 genome, 69 genes that overlapped with or were adjacent to the significant SNPs were identified as potential resistance genes to Fusarium ear rot. Comparing transcriptomes of the most resistant and most susceptible lines during the very early response to Fusarium ear rot, we detected many differentially expressed genes enriched for pathways related to plant immune responses, such as plant hormone signal transduction, phenylpropanoid bio-synthesis, and cytochrome P450 metabolism. More than one-fourth of the potential resistance genes detected in the GWAS were differentially expressed in the tran-scriptome analysis, which allowed us to predict numbers of candidate genes for maize resistance to ear rot, in-cluding genes related to plant hormones, a MAP kinase, a PR5-like receptor kinase, and heat shock proteins. We propose that maize plants initiate early immune responses to Fusarium ear rot mainly by regulating the growth-defense balance and promoting biosynthesis of defense compounds.