Fusarium head blight (FHB) is a devastating disease of wheat, which is influenced by weather conditions and agronomic factors. Since FHB is a mostly monocyclic disease, the quantity of primary inoculum is a key factor influencing the FHB incidence. To investigate the connection between the primary Fusarium inoculum and the final population on wheat ears, naturally occurring populations of Fusarium avenaceum, Fusarium culmorum, Fusarium graminearum, Fusarium poae and Microdochium nivale were studied at eight locations in Flanders, Belgium. To determine the composition of the primary inoculum in November 2008, gramineous weeds, wheat residues, maize residues and soil samples were examined. In July 2009, wheat ears were examined to gain insight into the composition of the population at the end of the growing season. Comparing both populations can give an indication to what extent the primary inoculum in November 2008 contributes to the final FHB population in July 2009. Fusarium species residing saprophytically on gramineous weeds and crop residues or species persisting in soil as chlamydospores certainly contribute to the primary inoculum that will lead to infection of cereal crops grown on that field. Knowledge of the correlation between the primary inoculum and the composition of the FHB population at the end of the growing season can be important to predict the occurrence of FHB contamination and to implement control strategies for Fusarium Head Blight.