Several species of benthic macro and meio-invertebrates actively emerge from the seabed to the water column during the night. Such diel vertical migrations have important consequences for benthic-pelagic coupling, dispersal, connectivity and recovery after disturbance of benthic assemblages. However, this process has never been studied in the coast of the Humboldt Current ecosystem. Herein we examined the relationship between the emerging assemblage and moon phases (and co-variables) and the timing of emergence during the day/night cycle, in a sublittoral soft-bottom habitat. Sampling using emergence traps was conducted at 7. m depth in the zone of Bolsico, a sheltered cove with low bottom hydrodynamics in northern Chile. Multivariable analysis showed that changes in the dissimilarity of the emerging assemblage were related to each moon phase. The percentage of moon illumination, bottom illumination and tide amplitude explained most of the variation of the emerging assemblage. Species showed differential responses to each moon phase; some were abundant at intermediate phases (e.g., harpacticoids), or peaked at full moon (e.g. ostracods) and others such as mysids emerged in equal abundances at all moon phases. The timing of assemblage emergence followed a consecutive sequence through the night/day period. Most of the studies dealing with the emergence processes have described species-specific responses. Our research shows that the examination at assemblage level may reveal new and distinct patterns of emergence in sublittoral soft-bottom habitats.