Motile cryptofauna living in dead coral rubble represent some of the greatest biodiversity and basal energetic resources on tropical coral reefs. Yet we know relatively little about how and why coral rubble cryptofauna communities change over space and time. As human impacts increase the degradation of living hard corals to dead coral rubble on many reefs worldwide, understanding the communities that will succeed in these degraded environments and the factors paramount to their success becomes increasingly central to coral reef ecology and conservation. Using a remote and uninhabited oceanic atoll in the Pacific Ocean, we quantified the natural spatial variability in motile cryptofauna diversity and community structure in coral rubble across scales (m to km) and tested whether variability at smaller scales could be explained by gradients in microhabitat. We show that coral rubble cryptofauna communities are most variable at intra-site scales (m) rather than inter-site scales (100s m) or between reef zones (km scales). We also show that a substantial amount of variation in cryptofauna density (55%) and phyla-level community structure (31%) is explained by small-scale habitat characteristics, specifically the substrate type below the rubble and the variability in macroalgal cover on individual rubble pieces. Our findings highlight the need to study small-scale processes that are relevant to motile cryptofauna and their community interactions if we are to elucidate the structuring forces of these diverse cryptic assemblages on coral reefs.