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A broad range of different Fusarium (F.) species is associated with Fusarium head blight (FHB) on barley and the corresponding negative effects in downstream processing of barley grain in food and feed production. Previous studies highlight the significance of the wheat-relevant and well-studied species F.graminearum as well as less prominent species including F.culmorum, F.avenaceum, F.tricinctum, F.langsethiae, F.sporotrichioides, F.poae, and others. In this context, prevalent climate and cultivation conditions were shown to determine disease severity as well as dominance of certain species within the Fusarium pathogen complex. To gain further insight into possible historic developments of FHB, the annual occurrence of currently relevant Fusarium species was analyzed in Bavarian archive samples of winter (from 1958 to 2010) and spring barley (from 1965 to 2010) using species-specific quantitative polymerase chain reaction. Although DNA contents varied between samples of individual years, data suggest a general increase in Fusarium incidence, particularly in spring barley. Comparing pathogen complexes, we observed not only continuous dominance of F. graminearum in winter barley, but also an increasing relevance of this species in spring barley. The rising Fusarium incidence over time generally coincides with climate change related factors like increasing temperatures. However, it may furthermore be linked to changing cultivation methods and intensified maize production. This study therefore exhibits the dynamic complexity of barley grain contamination with Fusarium spp., which should be taken into account for future disease management.