All data and code associated with this manuscript are freely available in the Dryad Digital Repository.

Ecological patterns in biodiversity are primarily based on conspicuous organisms. Few methods are used to survey the taxonomically rich cryptobiome, which is made up of inhabitants from within microhabitats. One way that cryptic marine biodiversity can be non-invasively surveyed is by analyzing environmental DNA (eDNA) present in seawater. Using coral reefs as a model system, here we compare estimates of cryptic diversity among community biomass and eDNA metabarcoding sampling methods with a broad eukaryotic marker...