The objective of this study was to investigate the stability, across well‐differentiated environments, of genetic control of maize resistance to Fusarium graminearum and Fusarium verticillioides ear rots and mycotoxin contamination, found in genotypes of diverse origin and adapted to different environments. This knowledge will help to design the most appropriate breeding programme to reduce mycotoxin content across a wide range of environments. Although maize genetics involved in resistance to ear rots and mycotoxin contamination greatly depended on the environment, additive and dominance effects were the predominant genetic effects in most environments. The stability across environments for resistance to ear rots and deoxynivalenol and fumonisin contamination was low, and recommended target areas of breeding programmes for either Fusarium species are different based on the different nature of genetic effect × environment interactions for each species. In general, the classification of inbreds and hybrids according to their resistance levels was similar across environments, suggesting that the same sources of resistance could be suitable for different environments, and breeding for resistance to one species would affect resistance to the other one.