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Maize ear rot, one of the most destructive diseases in summer‐sown maize areas of China, is caused by several Fusarium spp. Not only does this pathogen lower maize yields, but also negatively impacts both animal and human health through the production of fumonisin mycotoxins. In this study, we collected 472 unique isolates of F. verticillioides from 480 samples of maize ear rots across eight Chinese summer‐sown maize regions and evaluated their genetic variability and aggressiveness. Analysis of polymorphic intersimple sequence repeat (ISSR) loci revealed high levels of genetic variation, particularly in Henan and Shandong provinces. The STRUCTURE result showed that all F. verticillioides isolates clustered into three populations, rather than eight distinct geographical provinces, and there was no significant positive correlation between genetic distance and geographical distance. Most of the variation resulted from genetic differences within rather than between populations. Pathogenicity varied among the evaluated F. verticillioides isolates, and most isolates examined, caused a moderate level of disease; there was no strong correlation between pathogenicity and genetic diversity. This is the first comprehensive report of both the genetic variability and pathogenicity of F. verticillioides across the whole summer‐sown maize region in China. These results provide important information that can inform efforts to control maize ear rot and fumonisin contamination caused by F. verticillioides. [ABSTRACT FROM AUTHOR]