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Abstract:To investigate the vertical zonation in the copepod community in relation to stratified water-masses, multi-layer sampling at 1-2-m intervals using a submersible pump was conducted on 6 August 2009 in the inner part of Tokyo Bay, central Japan. Acartia sinjiensis showed a peak of the population density in the surface water, which was influenced by river discharge, and Paracalanus parvus s.l. had a peak contrastingly in the mid layer, which was intruded by coastal water from out of the bay through estuary circulation. Calanus sinicus occurred in the coastal water layer with other oceanic copepods. The most dominant species, Oithona davisae showed a remarkable peak in the pycnocline in the 3-6-m layer. Adults of Labidocera rotunda and Pseudodiaptomus marinus and immature copepodids of Hemicylops japonicus accumulated just above the hypoxic bottom-water (DOϽ1.0 mg L Ϫ1 ). The shallower peak of the bimodally distributed Acartia omorii was very sharp and seemed to be formed by predation by the moon jellyfish Aurelia aurita s.l. on the copepods in the layers above and below the peak. The vertical zonation in the copepod community were reflected by the characteristic environmental conditions in Tokyo Bay in the summer, i.e. estuary circulation, hypoxia in the bottom layer and the distribution of jellyfish.