Declining oxygen concentrations in aquatic habitats represent extreme conditions that threaten benthic life. Hypoxia has recently become an important research topic, as areas affected by these phenomena are spreading globally. Omura Bay is one of the most highly enclosed seas in Japan, and severely hypoxic conditions occur at the bottom every summer. We conducted a preliminary study in the center of the bay to evaluate how seasonal hypoxia affects the abundance and community composition of benthic meiofauna, with particular reference to copepods. The copepod densities and their nauplii differed significantly among seasonal categories (before, during, and after hypoxia). Furthermore, the degree of the seasonal decline in copepods during hypoxia seemed much more severe than that in nematodes, the most abundant meiofauna. The assemblages of adult copepods had the simplest composition during hypoxia, when harpacticoid copepods in the family Cletodidae, which have smaller and slender bodies, occurred at significantly higher frequencies (a contribution of 84% to the mean similarity among seasons). After hypoxia, the relative abundance of copepods in the families Ectinosomatidae and Longipediidae increased, which may likely be attributed to their higher swimming abilities and rapid recruitment via specific planktonic nauplius stages, respectively. High frequencies of copepods in the Cletodidae family have also been observed under hypoxic conditions in the Mediterranean Sea, suggesting that similar processes affect benthic copepod communities, which work to the advantage of cletodid species with small and slender forms in the subtidal sediment bottom under severe hypoxia in Omura Bay and other regions.