A growing awareness of a subsurface fossil record of mostly hyphal fungi organisms stretching back through the Phanerozoic to approximate to 400 megaannum (Ma) and possibly earlier, provides an alternative view on hyphal development. Parallel with the emergence of hyphal fungi during Ordovician-Devonian times when plants colonized the land, which is the traditional notion of hyphal evolution, hyphae-based fungi existed in the deep biosphere. New insights suggest that the fundamental functions of hyphae may have evolved in response to an ancient subsurface endolithic life style and might have been in place before the colonization of land. To address the gaps in the current understanding of hyphal evolution a strategy based on research prospects involving investigations of uncharted geological material, new diagnostics, and comparisons to live species is proposed.