Fungi are an important constituent of microbial endolithic assemblages in marine ecosystems. As euendoliths, they penetrate limestone, mollusk shells and other carbonate substrates, where they can exploit mineralized organic matter, attack their hosts, or engage in symbiotic relationships. They leave specific boring traces, which can be identified in the fossil record and described as trace fossils. Their distribution is independent of light and extends from the intertidal ranges to abyssal oceanic depths. Important, but insufficiently studied, is the role of aggressive endolithic fungi in skeletons of corals where they are ubiquitous and globally distributed. In healthy growing reef corals, the relationship between the coral coelenterate, endolithic algae and fungi is in a state of equilibrium, but can turn detrimental to coral health when reefs are exposed to environmental stress.