Glomeromycotan spores from the Lower Devonian Rhynie chert provide the first evidence for germination shields in fossil fungi and demonstrate that this complex mode of germination was in place in some fungi at least 400 million years ago. Moreover, they represent the first direct marker relative to the precise systematic position of an Early Devonian endomycorrhizal fungus. In extant fungi, germination shields occur exclusively in the genus Scutellospora (Glomeromycota: Diversisporales, Gigasporaceae). These structures are regarded as a derived feature within the phylum Glomeromycota, and hence their presence in the Rhynie chert suggests that major diversification within this group of fungi occurred before the Early Devonian.