On the southeastern Bering Sea shelf, mesozooplankton plays an important role in material transfer between primary producers and fisheries resources. The biomass of mesozooplankton in this region is known to vary annually, but little is known about annual changes in community structure and species composition. In the present study, regional and long-term changes in abundance, biomass and community structure of copepods and chaetognaths on the shelf were evaluated based on NORPAC net samples collected during summers of 1994-2009. During the study period, regime shifts occurred from high interannual variability regime (1994-1999) to low interannual variability regime with high temperature (2000-2005), then to a low interannual variability regime with low temperature (2007-2009). A total of 24 calanoid copepod species belonging to 21 genera were identified from samples. Copepod abundance ranged from 150 to 834,486 inds. m(-2), was greatest on the Middle shelf, and was higher in cold years, than in warm years. Copepod biomass ranged from 0.013 to 150 g DM m(-2), and was also higher in cold years than in warm years. Based on the results of cluster analysis, the copepod community was divided into six groups (A-F). The regional and interannual distributions of each group were distinct. Interannual changes in abundance of the dominant copepod on the Outer shelf and Middle shelf were highly significant (p < 0.0001), and their abundances were negatively correlated with temperature and salinity. Interannual changes in copepod community that occurred between cold and warm years are thought to have been caused by differences in the magnitude and timing of the spring phytoplankton bloom between the two regimes. Abundance and biomass of the chaetognath Parasagitta elegans ranged from 30 to 15,180 inds. m(-2) and from 11 to 1559 mg DM m(-2), respectively. Chaetognath abundance was significantly correlated with the abundance of the dominant copepods (p < 0.0001). Differences in cold and warm years may also affect recruitment of walleye pollock. We conclude that on the southeastern Bering Sea shelf, the magnitude and timing of primary production, which is related to climate change, may significantly affect how it is transferred through the food web.