The production of H-2 in hydrothermal systems and subsurface settings is almost exclusively assumed a result of abiotic processes, particularly serpentinization of ultramafic rocks. The origin of H-2 in environments not hosted in ultramafic rocks is, as a rule, unjustifiably linked to abiotic processes. Additionally, multiple microbiological processes among both prokaryotes and eukaryotes are known to involve H-2-production, of which anaerobic fungi have been put forward as a potential source of H-2 in subsurface environments, which is still unconfirmed. Here, we report fungal remains exceptionally preserved as fluid inclusions in hydrothermal quartz from feeder quartz-barite veins from the Cape Vani Fe-Ba-Mn ore on the Greek island of Milos. The inclusions possess filamentous or near-spheroidal morphologies interpreted as remains of fungal hyphae and spores, respectively. They were characterized by microthermometry, Raman spectroscopy, and staining of exposed inclusions with WGA-FITC under fluorescence microscopy. The spheroidal aqueous inclusions interpreted as fungal spores are unique by their coating of Mn-oxide birnessite, and gas phase H-2. A biological origin of the H-2 resulting from anaerobic fungal respiration is suggested. We propose that biologically produced H-2 by micro-eukaryotes is an unrecognized source of H-2 in hydrothermal systems that may support communities of H-2-dependent prokaryotes.