Present-day sphenophytes, i.e. the species of the genus Equisetum, are hosts to a variety of fungi. Although the Sphenophyta have a long evolutionary history and were far more diverse in the past than they are today, little is known about fungi associated with the fossil representatives of this group of free-sporing vascular plants. A permineralized Sphenophyllum stem from the early Permian Autun Basin in France contains several types of fungal remains in the xylem and periderm, including a Perexiflasca-like chytrid thallus, blastic inflations of hyphal tips resembling simple glomoid spores, basidiomycete hyphae with clamp connections, and compact, three-dimensional hyphal structures of unknown function and systematic affinity. Cell wall appositions in the periderm are evidence that at least one of the fungi colonized the stem while it was alive. A taphonomic peculiarity are trace fossils of hyphae in tracheids filled with an amber-colored to brown substance, perhaps a type of gum. This is only the second report of fungi from the aerial parts of a fossil sphenophyte. It adds to the growing body of evidence that diverse fungal communities were associated with the iconic plants of the Carboniferous and early Permian coal swamp forests.