Compositions of Aspergillus flavus populations determine the extent to which crops become contaminated with aflatoxins. In the current study, influences of diverse crop hosts on competition among A. flavus isolates were quantified with pyrosequencing. Maize, cotton, soyabean and sorghum supported different levels of sporulation, but intraspecific differences in sporulation were not detected on any host. However, hosts differentially influenced competition during infection, allowing greater sporulation by some isolates and increased host tissue invasion by others. Furthermore, competitive interactions during host invasion did not predict isolate success during sporulation. Isolates were similarly competitive on maize and sorghum, the two most closely related hosts. Host-specific influences on intraspecific competition may dictate compositions of A. flavus populations and, as a result, the severity of aflatoxin contamination. Host factors should be considered when designing and implementing aflatoxin management strategies including biocontrol with atoxigenic strains.