Diverse micro‐organisms populate a global deep biosphere hosted by rocks and sediments beneath land and sea, containing more biomass than any other biome except forests. This paper reviews an emerging palaeobiological archive of these dark habitats: microfossils preserved in ancient pores and fractures in the crust. This archive, seemingly dominated by mineralized filaments (although rods and coccoids are also reported), is presently far too sparsely sampled and poorly understood to reveal trends in the abundance, distribution, or diversity of deep life through time. New research is called for to establish the nature and extent of the fossil record of Earth's deep biosphere by combining systematic exploration, rigorous microanalysis, and experimental studies of both microbial preservation and the formation of abiotic pseudofossils within the crust. It is concluded that the fossil record of Earth's largest microbial habitat may still have much to tell us about the history of life, the evolution of biogeochemical cycles, and the search for life on Mars.