Oxygen minimum zones (OMZs) are characteristic of highly productive upwelling ecosystems and create unique conditions for benthic organisms that can adapt to hypoxic conditions and high quantities of organic material. Community structure, macrobenthic organism diversity, and biomass of giant filamentous bacteria (Candidatus Marithioploca) were studied along a bathymetric gradient from 79 to 935 m, including depths within and below the OMZ. Sediment samples were taken in both Huacho (11°S) and Callao (12°S) on the central coast of Peru using a van Veen grab sampler and multi-corers in October and November 2008. In addition to the biomass of Candidatus Marithioploca, the abundance, biomass, species richness, and structure of the macrobenthos were estimated on the surface as well as in the sediment column (i.e., 0–1, 1–2, 2–5, and 5–10 cm). The results indicate that, within the OMZ, there was a lower abundance and biomass of the macrobenthos but higher biomass of Candidatus Marithioploca. Within the OMZ, polychaetes were the dominant group, whereas below the OMZ, a diversity of taxonomic groups was recorded. The community structure reflects the gradient at depth as dissimilarity increases with depth. Diversity and evenness were lower within the OMZ and higher below the OMZ. The consistency of this pattern stands when compared to macrobenthos in the OMZ of other regions. The results of the present study highlight the importance of the OMZ as a modifying factor of benthic composition along depth gradients, particularly in diversity patterns.