Christmas Island and the Cocos (Keeling) Islands represent a unique marine biodiversity hotspot because of the overlap between two major biogeographic provinces (Indian and Pacific Ocean) and the high proportion of endemic species. In this paper, we compile existing scientific literature pertaining to marine organisms and environments at these islands to determine the current state of knowledge and identify major knowledge gaps. In total, 1066 studies have been published, including 582 peer-reviewed journal articles (55% of all publications), 332 reports, 141 books or book chapters, and 11 theses. These studies extend back to 1697, but most (83%) are post-1970. Seabirds have been the most studied group (43% of all publications), followed by land crabs (13%). There has been very little research on plankton (<0.3% of all studies), despite the diversity of marine species that have larval stages (including land crabs) and the importance of plankton to ecosystem function. Most invertebrate groups have received little attention or have not been studied. The taxonomic bias in marine research at these islands means that most of the invertebrates are yet to be documented. Some of these groups (e.g., Polychaeta, Copepoda, and anchialine fauna) are known for their high degree of endemism and are likely to contain new species, thereby increasing the biodiversity value of the islands. That whole families (even phyla) are yet to be studied highlights the infancy in some areas of marine research and adding to species lists for unstudied or understudied groups is one priority that would increase the conservation importance of these islands. Without this knowledge, the ability to monitor, detect or predict anthropogenic impacts on marine species is severely restricted, and therefore limits the development of management strategies aimed at conserving the unique marine biodiversity of these islands. Further studies on functional processes and research related directly to impacts are also needed. Increasing studies that directly relate to management questions will provide guidance to managers charged with protecting the environment. Improved decision making in conservation management will occur through increased directed research and monitoring.