Coral reefs are one of the most diverse marine ecosystems. Most of the reef biodiversity is comprised of small organisms that inhabit small cryptic spaces within the reef framework - the cryptobiome. The knowledge of these assemblages is in its infancy as it has traditionally been overlooked in reef assessments. To gain an understanding of the cryptobiome in the Red Sea, molecular approaches have been combined with standardized protocols using Autonomous Reef Monitoring Structures. This has enabled the knowledge on the distribution patterns of the cryptobiome on various spatial scales ranging from within reef to basin wide. As well as spatial patterns the use of standardized methods have enabled robust assessments of how the cryptobiome changes temporally, including as a response to coral bleaching events. Future research should be focused on understanding the functions of the cryptobiome and their symbiotic relationships with the surrounding benthic habitats. Including the cryptobiome in monitoring efforts will give a more holistic overview of the functioning of the reef system and aid in preserving reefs for future generations.