Coral reefs are considered to be the rainforests of the sea. They support an estimated 25% of all marine life even though they represent about 0.2% of the ocean's surface. They are regarded as the most diverse marine habitat, yet our knowledge of the diversity within coral reef ecosystems is severely limited. The number of species associated with coral reefs is estimated to range from one to ten million. Current understanding and assessment of reef biodiversity is largely limited to the well-known and accessible biota that exist on the surface of reefs, especially fishes and corals, even though these taxa represent just a small fraction of reef diversity. Most of the diversity of reefs is found within the complex architecture of the reef matrix and not in the organisms (corals and algae) that create the three-dimensional structure. The diverse community of organisms that live inside the reef matrix is collectively known as cryptobiota. CRED is working towards monitoring the cryptobiota with autonomous reef monitoring structures (ARMS).

Compounding our lack of knowledge on the biodiversity of coral reefs is the concern that coral reefs are among the most-threatened ecosystems because of the effects of natural events and human activities. Coral reef ecosystems are highly susceptible to local effects, such as exploitation, pollution, and habitat destruction, and global effects, such as climate change and ocean acidification. Changes in marine biodiversity are a direct reflection of these effects, and much reef biodiversity could be lost before it is even documented.