Abstract: 14 different resistant varieties were selected from a set of 25 maize varieties via identification and survey. The RAPD analysis for the 14 varieties, 20 samples (6 varieties including infected and healthy plant), was conducted via PCR amplification. The results show that maize varieties are genetically highly diverse. The 20 samples are divided into 7 lineages based on DNA label number at a rescaled distance cluster combination of 15. The variety resistances are highly similar within same lineages. Regarding inheritance, the 6 infected plants (infected by Fusarium subglutinas) are quite different from the healthy ones of same varieties. Field experiments show that rotation planting resistant and susceptible varieties has a significant controlling effect on the occurrence of maize top-rot disease. This resolves the problem of serious maize top-rot disease in continuous planting of maize for several years.