Cultural layers from early medieval strongholds in Pszczew and Santok have been examined for the presence of pollen grains and spores as well as residues of fungi. The presence of the following remains has been recorded: fossil hyphopodia of Gaeumannomyces, teliospores of Puccinia, spores of Bipolaris, Thecaphora and Tilletia, teliospores of the genus Urocystis, Ustilago and Uromyces, ascocarps (perithecium) of the Ascomycota or the pycnidium of Sphaeropsidales. A greater diversity and abundance of fungi spores sensu lato was recorded in Santok, as compared to Pszczew. Both early medieval sites recorded a significant proportion of cereal pollen, including Secale cereale. It remains an undisputed fact that the grains and other plants collected in both strongholds were strongly infected with fungi. The analysis of the cultural layers for the presence of fungi remains provides significant data on the presence of certain species of plants and their growth conditions in natural environments and in agriculture.