The 0- to 1000-m vertical distribution patterns of micronekton and macrozooplankton were determined in the Costa Rica Dome region (9° N; 90° W) of the Eastern Tropical North Pacific in October–November 2007 and December 2008–January 2009. The area has a pronounced oxygen minimum zone (OMZ) that impacts the distribution of both migrating and mesopelagic species. Sampling was conducted at a relatively fine scale (mesopelagic depth intervals as small as 25 m) within ecologically relevant strata to assess how this hydrographic environment influenced the structure of these groups. Zooplankton were collected in vertically stratified Multiple Opening/Closing Net and Environmental Sensing System tows during the day and the night, and abundances were analyzed in association with variations in oxygen concentration, temperature and depth. Each vertical stratum of the water column was a unique ecological zone with a specific community makeup. The upper and midwater column (0–550 m) was strongly influenced by diel vertical migration patterns, particularly the daytime descent of euphausiids and myctophid fish into the core of the OMZ. Distinctly different communities occurred below the OMZ core. The lower oxycline (LO) (∼500–700 m depth range) was dominated by Cyclothone spp. fish as well as a diverse population of other taxa, often aggregated into a discrete layer (25 m thick), particularly in 2008. In the suboxycline (>700 m depth range), the community shifted to typical bathypelagic taxa. These finer scale vertical patterns provided new insight into the ecological structure of OMZs, revealing the unique layering at the LO and differential impacts on diel vertical migrators.