Coral microbiology research has long focused on the composition and functional roles of prokaryotic organisms, but microeukaryotic communities, including the enigmatic fungi remain a poorly understood “black box” within coral and other holobionts. Here, we summarise what is known and hypothesised about the diversity, functional traits and potential, and chemodiversity of coral- and reef-associated fungi and fungi-like organisms (FLOs). Finally, we briefly outline the challenges associated with the characterization of marine fungi and provide a perspective for future studies to elucidate the biology, chemical ecology, and organismal interactions of marine fungi and FLOs within coral reef holobionts and their potentially far-reaching roles in coral reef ecosystem functioning and health.