Fusarium (FER) and Gibberella ear rots (GER), caused by a cortege of Fusarium species, are the two most devastating diseases of maize (Zea mays L.), reducing yield and affecting grain quality worldwide, especially by contamination with mycotoxins. The spectrum of Fusarium spp. that led to infections is likely to be shaped by environmental conditions such as temperature, moisture or drought stress, but also by agricultural practices, including tillage, irrigation, crop rotation or plant variety. Ongoing climate change (CC) is already impacting the distribution and prevalence of different Fusarium species. This can lead to shifts in the dominant pathogens causing FER and GER under various cropping systems, potentially altering the mycotoxin profiles observed in maize grain. In this context, the use of agricultural CC mitigation practices could also be questioned in regard to population pathogens evolution. Understanding the modulation of FER and GER pathogens populations to the combined pressures of CC and evolving agricultural practices is essential for predicting the emergence and/or spread of epidemics. The aim of the present study was to describe the representativeness of Fusarium species on maize kernels in various agronomical contexts, including soil type, irrigation management, and geographical location, over a period of 2 years, using a metabarcoding approach targeting the specific EF1 alpha region. This description will allow for the identification of key factors driving the risk of FER and GER and associated mycotoxin contamination.