Fusarium verticillioides can be transmitted via seeds and cause systemic infection in maize (Zea mays L.); its mycotoxin has harmful effects on animal and human health. We combined QTL mapping in recombinant inbred line (RIL) populations with a genome-wide association study (GWAS) of 217 diverse maize lines using 224,152 single nucleotide polymorphisms (SNPs) under controlled conditions to determine the genetic architecture of F. verticillioides seed rot (FSR) resistance. Our study identified 8 quantitative trait loci (QTLs) and 43 genes associated with 57 SNPs that were correlated with FSR resistance through linkage mapping and GWAS, respectively. Among these, there were three candidate genes, namely GRMZM2G0081223, AC213654.3_FG004, and GRMZM2G099255, which were detected in both linkage mapping and GWAS. Furthermore, the near-isogenic lines (NILs) containing GRMZM2G0081223, which also had a susceptible parent background, were found to have a significantly improved level of resistance. In addition, the expression profile of the three candidate genes revealed that they all respond to the infection following inoculation with F. verticillioides. These genetic analyses indicate that FSR resistance is controlled by loci with minor effect, and the polymerization breeding of lines with beneficial alleles and candidate genes could improve FSR resistance in maize.Maize is one of the most important cereals in the world due to its high yield potential and its high demand for use as food, feed, and for industrial purposes. Maize is subject to a variety of biotic and abiotic stresses during its lifetime, which can significantly affect final yield and quality. The planting area for maize in China is 37.07 million hectares, of which the Huang-Huai-Hai region accounts for 39%. In this region, the incidence of soil-borne diseases in maize has increased over the years, which coincides with increases in the use of cultivation systems such as double cropping, no-tillage, and straw returned. Fusarium verticillioides (formerly Fusarium moniliforme), which is a commonly-found soil-borne fungal species, can be transmitted to seeds and cause systemic infection in maize 1 . Previous studies have confirmed that seeds infected with F. verticillioides are a source of root and stalk infection 2 . In addition, the fungus can be transmitted from the planted seed through to the developing kernels via the mature plant 1,[3][4][5] . The diseases caused by F. verticillioides include seedling blight, stalk rot, root rot, kernel rot, ear rot, and seed rot 5,6 . F. verticillioides infection can result in decreased grain yields, poor grain quality, and contamination by the mycotoxin fumonisin 7 . The fumonisins produced by F. verticillioides are known to cause a variety of diseases when ingested by animals, and have been implicated in human carcinogenesis and neural tube defects, as well as in plant diseases 6 .