Coral reef cryptofauna (coelobites) are metazoans that occupy the hidden recesses formed by structural taxa such as corals. While cryptic communities are thought to account for the majority of reef biodiversity and play important roles in reef trophodynamics, little empirical evidence exists supporting these claims. Quantitative sampling of coelobites has been thus far limited due to highly heterogeneous reef topographies as well as difficulties associated with identification of large numbers of species. In the eastern Pacific, monogeneric stands of Pocillopora form reef structures that are homogeneous across a horizontal plane and support a relatively depauperate fauna, thereby permitting detailed multispecies analysis. Sampling of motile cryptofauna associated with live coral and dead coral frameworks typifying four levels of degradation, was conducted at Playa Larga Reef on Contadora Island in the eastern Pacific, Gulf of Panamá. Communities associated with live coral colonies were less diverse than those associated with dead corals and the species richness of cryptofauna living on dead coral substrates was higher in more degraded habitats. Living coral colonies, however, support significantly greater densities of cryptofauna and more biomass per volume substrate than their dead coral counterparts. On dead coral frameworks, numbers of individuals and biomass were significantly greater per volume in areas of intermediate degradation. A field experiment was conducted to test the effects of flow, porosity and coral cover on cryptic communities associated with artificial reef frameworks (ARFs). Coral cover (live vs. dead) was not observed to affect the structure of communities occupying underlying frameworks, however, lower porosity substrates sheltered greater abundances of individuals per volume substrate and low flow environments supported elevated biomass. Additionally, porosity and flow were both found to significantly affect relative species abundances as well as overall community diversity. Data from quantitative sampling of natural reef environments and experimental manipulation of cryptic reef habitats suggest novel and unexplored responses to mass coral mortality and reef habitat degradation. Coral death is considered to be vital to the maintenance of reef ecosystem habitat and biotic diversity. Contrary to the popular paradigm that a healthy reef ecosystem has high coral cover, the most diverse reef ecosystems are those which have experienced intermediate levels of degradation. Furthermore, while living corals support elevated cryptofauna abundances and biomass, the magnitude of communities associated with dead framework materials suggest that abundant cryptofauna populations persist in highly degraded reef environments.