Fusarium species are among the most important fungal pathogens of maize, where they cause severe reduction of yield and accumulation of a wide range of harmful mycotoxins in the kernels. In order to identify the Fusarium species and their mycotoxin profiles associated to maize ear rot and kernel contamination in Iran, a wide sampling was carried out from field in ten major maize-producing provinces in Iran, during 2015 and 2016. From 182 samples of maize kernels, 551 strains were isolated and identified as belonging to Fusarium genus. Among the 234 representative strains identified at species level by translation elongation factor (EF-1α) sequences, the main Fusarium species were F. verticillioides and F. proliferatum, together representing 90% of the Iranian Fusarium population, and, to a lesser extent, F. incarnatum equiseti species complex (FIESC), F. thapsinum and F. redolens. Fumonisin (FBs) production by F. verticillioides and F. proliferatum representative strains was analysed, showing that all strains produced FB₁. None of F. verticillioides strains produced FB₂ nor FB₃, while both FB₂ and FB₃ were produced only by F. proliferatum. Total mean of FBs production by F. verticillioides was higher than F. proliferatum. The occurrence of different Fusarium species on Iranian maize is reason of great concern because of the toxigenic risk associated to these species. Moreover, the diversity of the species identified increases the toxigenic risk associated to Fusarium contaminated maize kernels, because of the high possibility that a multi-toxin contamination can occur with harmful consequences on human and animal health.