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Several hypotheses of how zooplankton communities respond to coastal hypoxia have been put forward in the literature over the past few decades. We explored three of those that are focused on how zooplankton composition or biomass is affected by seasonal hypoxia using data collected over two summers in Hood Canal, a seasonally-hypoxic sub-basin of Puget Sound, Washington. We conducted hydrographic profiles and zooplankton net tows at four stations, from a region in the south that annually experiences moderate hypoxia to a region in the north where oxygen remains above hypoxic levels. The specific hypotheses tested were that low oxygen leads to: (1) increased dominance of gelatinous relative to crustacean zooplankton, (2) increased dominance of cyclopoid copepods relative to calanoid copepods, and (3) overall decreased zooplankton abundance and biomass at hypoxic sites compared to where oxygen levels are high. Additionally, we examined whether the temporal stability of community structure was decreased by hypoxia. We found evidence of a shift toward more gelatinous zooplankton and lower total zooplankton abundance and biomass at hypoxic sites, but no clear increase in the dominance of cyclopoid relative to calanoid copepods. We also found the lowest variance in community structure at the most hypoxic site, in contrast to our prediction. Hypoxia can fundamentally alter marine ecosystems, but the impacts differ among systems.