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Over an eight-year period, 686 winter wheat grain samples and information on their cropping history were obtained from Swiss growers. To estimate the risk of Fusarium head blight (FHB), grains were examined for Fusarium species incidence, mycotoxin content as well as the abundance of F. graminearum (FG) and F. poae (FP) DNA and three chemotypes, 15-acetyl-deoxynivalenol (15ADON), 3-acetyl-deoxynivalenol (3ADON) and nivalenol (NIV). Of all Fusarium species, FG and FP were predominant, and the average abundance of the FG DNA was three times higher compared with that of FP. The average detection of the 15ADON chemotype was twice as high as those of 3ADON and NIV, respectively. Deoxynivalenol (DON), zearalenone (ZEA) and nivalenol (NIV) were the most frequently detected toxins. For DON, 11% and for ZEA, 7% of all samples exceeded the European maximum limits for unprocessed cereals intended for human consumption. Furthermore, NIV was most likely produced by four different Fusarium species. A multiple correspondence analysis revealed that high levels of FG and DON were mainly observed in grain samples from fields with the previous crop maize, reduced tillage, cultivars with poor FHB resistance and strobilurin-based fungicides. Other previous crops and/or ploughing decreased the DON content by 78 to 95%. ZEA showed a similar pattern. In contrast, high levels of FP and NIV were associated with samples from ploughed fields and the previous crop canola. These findings and the negative correlations between FP DNA and FG incidence, ZEA and DON suggest a different ecological niche for FP or diverging requirements for growth and infection.