Coral reefs are globally significant repositories of marine biodiversity. Over 25% of all marine life depends on coral reefs at some point in their life cycle. Among the nine million species that live on the world’s coral reefs, many are undescribed. Climate change has emerged as an immediate threat to the survival of both described and undescribed species, disrupting the ecological integrity of coral reefs and jeopardising the livelihoods of millions of people who depend on them. The risk of biodiversity silently slipping away on coral reefs increases simultaneously with the scale and frequency of climate and anthropogenic threats. More targeted research is needed to understand the form and function of biodiversity and the extent and pace at which resident flora and fauna disappear. The development of environmental DNA (eDNA) approaches, i.e. the recovery of genetic information from environmental samples, provides exciting opportunities to revolutionise coral reef biodiversity monitoring and our ability to document the extent and rate of change in complex ecosystems. This chapter provides an overview of the field of eDNA and its strengths and challenges, focusing on metabarcoding and its relevance to biodiversity monitoring in coral reef ecosystems with a glimpse into future uses of novel eDNA technologies.