We present evidence that eukaryotic life has existed in an extreme environment, inside the oceanic crust. Up to now only prokaryotes have been discovered within deep marine sediments and glass-rims of pillow basalts, no higher life forms are described as yet. This study demonstrates unique filamentous fossil structures observed within carbonate-filled vesicles of a massive lava flow unit from the upper oceanic crust in the North Pacific (ODP Site 1224). Based on morphological traits including branching, septa and central pores, the filaments are interpreted as fungi. The chemical composition of the fungal structures differs from the surrounding crystalline carbonate matrix in the deep basaltic rocks. Small open space between the fungi and the carbonate cement and undisturbed filamentous growth through different calcite crystals indicate endolithic fungal growth after the calcium carbonate filling. The presence of euhedral pyrite crystals within the carbonate cements points out anaerobic conditions in this habitat. Our results provide for the first time evidence for eukaryotic, fungal life in deep ocean basaltic rocks.