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The spatial variation in zooplankton biomass, abundance and species composition in relation to hydrography and chlorophyll a (Chl a) was studied in the subarctic waters of Hudson Bay and Hudson Strait. Sampling was carried out in early September 1993 at 21 stations arranged along a transect following the Québec coast from James Bay, in Hudson Bay, to the vicinity of Ungava Bay in Hudson Strait. Both the biomass and the abundance of total zooplankton were low along the lower part of Hudson Bay (averaging 1.6 g DM m–2 and 9432 ind. m–2) and increased sharply toward the upper end of the Bay and in Hudson Strait (averaging 6.0 g DM m–2 and 40 583 ind. m–2). A total of 80 zooplankton taxa was identified in the samples. Copepods were clearly numerically dominant at all sampling stations, accounting for more than 85% and 93% of the zooplankton community in the Bay and the Strait, respectively. Clustering samples by their relative species composition revealed four groups distributed along well defined environmental gradients characterizing the distribution of physical variables and Chl a. The first group, located in the most southern region of Hudson Bay and farther offshore, northwest of the Belcher and Sleeper Islands, was strongly influenced by freshwater run-off from James Bay and other major rivers around the Bay, and was characterized by the presence of two euryhaline copepod species (Acartia longiremis and Centropages hamatus). The second and the third groups occupied the largest region along the sampling transect, from the middle of Hudson Bay to the western region of Hudson Strait, and were characterized by a typical arctic zooplankton fauna related to the cyclonic circulation in central Hudson Bay. The fourth group was located in the easternmost part of the sampling transect in Hudson Strait where the highest phytoplankton biomass values were observed (Chl a ~220 mg m–2). The zooplankton assemblage there showed an important increase in the abundance of the large herbivorous copepod Calanus glacialis/finmarchicus, which were numerically four times more abundant in the central Strait region (averaging 15 251 ind. m–2) than in the western side of Hudson Strait and in Hudson Bay (3629 ind. m–2). These results support the hypothesis that the structure in the local biological community is influenced by the local hydrodynamic features which, through their action on surface water temperature, salinity, stratification and mixing conditions, lead to spatial differentiation of the phytoplankton and zooplankton communities. [ABSTRACT FROM PUBLISHER]