Cryptic ecosystems of modern and ancient reefs contain substantial amounts of biodiversity. It remains uncertain, however, when and how metazoans adapted to such space. Early Cambrian reef systems witnessed the rise and fall of the earliest known cryptic sessile metazoans. Subsequent Middle Cambrian to Early Ordovician microbial-dominated reefs were generally devoid of true frame-building metazoans, as well as cryptic sessile fauna. The Early Ordovician microbial–siliceous sponge patch reefs of the Dumugol Formation, Korea represent one of the oldest in situ spiculate sponge-bearing cryptic communities exploiting intraskeletal cryptic environments. Less than half of these small millimeter- to centimeter-scale crypts contain low-diversity sessile cryptic assemblages of spiculate sponges and microbialites. The cryptic sponges that attach to the walls of the cavities or on top of internal sediments do not show any skeletal distortion at their contacts with host organisms. The spiculate sponges occur both in open spaces as well as in crypts, and are interpreted to be pioneers of intraskeletal crypts after the death of the cavity-providing organisms. The behavior of occupying transient cryptic habitats is interpreted as an incipient stage of sessile metazoan adaptation to a cryptic space by an opportunistic member of the epibenthic community. This resulted in the extension of the open surface community into crypts which occurred far in advance of the eventual establishment of obligate cryptic forms. The present study provides a critical link for establishing the origin and evolutionary history of early cryptic sessile metazoan adaptation.