Knowledge of benthic ecosystem response to ocean deoxygenation can be derived from the paleo-record, natural gradients, laboratory and mesocosm experiments and by using environmental proxies. Here I will focus on how natural oxygen gradients on upwelling margins associated with oxygen minimum zones offer tremendous insight into the consequences of ocean deoxygenation for benthic ecosystems. Changes in ecosystem structure include declines in biodiversity manifested as altered taxonomic composition, number and distribution of species, declines in body size, biomass and architectural complexity of taxa, as well as changes in vertical and geographic distribution. These structural changes are translated into altered ecosystem functions involving production, habitat provision, bioturbation, colonization potential and resilience, and trophic functions reflected in feeding modes, symbioses and carbon fixation pathways as well as visual behaviors, species interactions and bentho-pelagic coupling. Functional shifts are then manifested as altered ecosystem services. Fisheries may diminish under dysoxic conditions but flourish where individuals aggregate at hypoxic zone margins. Enhanced local C sequestration may emerge from limited remineralization and high deposition within OMZs or from carbonate precipitation under anaerobic methane oxidation, whereas stratification-induced nutrient limitation may ultimately limit atmospheric C drawdown. Genetic novelty in OMZs could fuel new industrial applications. Changes in greenhouse gases, habitat availability and species distributions create climate and hydrographic feedbacks that could further modify ecosystems. Exceedingly small increases or declines in oxygen (of 5 mMol kg-1 or less) can lead to state changes in benthic ecosystems when they are initiated at low oxygen concentrations. Thus, even small changes in oxygenation projected to occur in the next century may have large consequences on margins with oxygen minima. Our challenge is to identify where and when these will matter most and manage accordingly. In the majority of open ocean settings, oxygen rarely changes without concurrent shifts in temperature, CO2 and food supply. Understanding the interplay of these factors in shaping ecosystem structure, function and services is of increasing importance in a rapidly changing ocean.