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Maize ( L.) is a staple crop of economic, industrial, and food security importance. Damage to the growing ears by corn earworm [ (Boddie)] is a major economic burden and increases secondary fungal infections and mycotoxin levels. To identify biochemical pathways associated with native resistance mechanisms, a genome-wide association analysis was performed, followed by pathway analysis using a gene-set enrichment-based approach. The gene-set enrichment exposed the cumulative effects of genes in pathways to identify those that contributed the most to resistance. Single nucleotide polymorphism–trait associations were linked to genes including transcription factors, protein kinases, hormone-responsive proteins, hydrolases, pectinases, xylogluconases, and the flavonol synthase gene (in the maysin biosynthesis pathway). The most significantly associated metabolic pathways identified included those that modified cell wall components, especially homogalacturonan, wax esters, and fatty acids; those involved in antibiosis, especially 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), flavonoids, and phenolics; and those involved in plant growth, including N uptake and energy production. The pathways identified in this study, and especially the cell wall-associated pathways, identified here for the first time, provide clues to resistance mechanisms that could guide the identification of new resistant ideotypes and candidate genes for creation of resistant maize germplasm via selection of natural variants or gene editing.