Until recently, Fusarium fujikuroi was widely described as a non‐producer or a producer of little B‐series fumonisin toxins despite having a complement of fumonisin biosynthetic genes similar to those in F. verticillioides and F. proliferatum. Although high and low fumonisin‐producing F. fujikuroi strains have been shown to induce typical disease symptoms, the relationship between fumonisin production and virulence in F. fujikuroi has not been fully established. Following recent reports on the roles of bacterial endosymbionts in influencing the biology of their fungal hosts, including virulence, reproduction and the production of secondary metabolites, this study investigated the association of two strains of bacteria of the genus Enterobacter with a F. fujikuroi strain isolated from wheat in Nebraska. Results demonstrated the intracellular localization of bacteria within the hyphae of the fungus. The association with the bacteria was also correlated with macroconidia production and higher levels of virulence in the fungus. Additionally, fumonisin production was consistently and significantly (α = 0.05) higher in the bacteria‐containing F. fujikuroi strain compared with the bacteria‐free strain. Furthermore, higher levels of fumonisin production by bacteria‐containing F. fujikuroi correlated with higher expression levels of the fumonisin biosynthetic genes fum1, fum8 and fum21 under fumonisin‐inducing and non‐inducing conditions. Expression of fum15, which encodes a P450 monooxygenase, was similarly observed to be significantly (α = 0.05) higher in the bacteria‐containing fungus. Analysis of transcripts also revealed significantly (α = 0.05) higher expression of the sexual and asexual development activator protein, VeA, in the bacteria‐containing F. fujikuroi under fumonisin‐inducing conditions.