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Fusarium ear rot in maize (Zea mays L.) is a serious disease in all maize-growing areas worldwide. A total of 454 fungal strains were isolated from 69 commercial maize hybrids grown in Harbin, China, and comprised Fusarium subglutinans (34.8%), F. proliferatum (31.3%), F. verticillioides (20%), F. graminearum (9.7%), and F. equiseti (4.2%). Among them, a complex of multiple species, F. subglutinans, F. proliferatum, and F. verticillioides are the dominant fungi causing ear rot. Among 59 commercial maize hybrids, eleven hybrids (18.6%) were found to be highly resistant to Fusarium ear rot. Simple sequence repeat (SSR) analysis using six pairs of primers resulted in 24 reproducible bands and cluster analysis separated the maize hybrids into eight groups. There was little genetic variation associated with disease resistance. No correlation was found between genetic diversity and disease resistance.