Fungi within Aspergillus section Flavi are the most important causal agents of crop aflatoxin contamination. Aflatoxins are natural carcinogens that contaminate food and feed impacting human and animal health and trade. The extent of crop contamination is partly determined by the infecting species. A. flavus and A. parasiticus are often implicated as causal agents of aflatoxin contamination. Recently, species with S morphology capable of producing high levels of aflatoxins have been identified. Several aflatoxin-producers frequently co-occur in agricultural regions and may coinfect crops. The current study assessed interaction among fungi with S morphology, A. flavus L strain and A. parasiticus on maize at 25C and 30C. Proportions of infecting mycelia and spores of each species were quantified with quantitative pyrosequencing during co-infection. A. flavus dominated sporulation at both temperatures. Fungi with S morphology outcompeted A. flavus during infection and A. parasiticus, both during infection and sporulation at 30C. Sporulation was reduced during coinfection, but crop contamination with aflatoxins was not significantly reduced or enhanced. Results suggest that the nature of coinfecting fungi and temperature can influence the fungal population structure, with temperatures around 30C selecting for increases in S morphotype fungi. Efforts to develop aflatoxin management should consider influences of interacting fungi and shifting environmental temperature.