The structure of zooplankton communities has a significant impact on vertical flux of organic material and cycling of elements in the sea, thus climate-induced changes in zooplankton abundance and species composition have the potential to dramatically affect biogeochemical cycles. The West Antarctic Peninsula (WAP) is one of the most rapidly warming regions on Earth, with documented changes in temporal and spatial distribution of the zooplankton community, and in annual peak organic particle export as measured by sediment traps. During the Palmer, Antarctica Long-Term Ecological Research Program (PAL LTER) January 2009 summer cruise we had an opportunity to investigate the role that zooplankton community composition plays in the export of organic matter to depth (i.e., via grazing, fecal pellet production, and diel vertical migration). Clear patterns in zooplankton distribution included salps (pelagic tunicates) at the outer slope stations, significant krill numbers inshore, and a mix of krill and Limacina pteropods (pelagic snails) on the shelf. At an outer slope station we sampled a salp ‘bloom’ of a density two orders of magnitude higher than recorded by the PAL LTER thus far. Salp fecal pellet production experiments at this station indicate significant vertical flux of particulate organic carbon and nitrogen due to this massive salp bloom. Analysis of zooplankton fecal pellets in a time-series sediment trap deployed in the northern shelf region over the preceding year indicated krill fecal pellets dominate the particle flux, although what appear to be pellets from large copepods are also abundant. Diel vertical migration patterns were detected in salps and in some crustacea such as ostracods. By feeding in surface waters at night and metabolizing their food at depth in the day these taxa may actively transport organic matter to depth. Although preliminary, our results suggest that long-term observed or predicted changes in zooplankton community composition in the WAP, such as the decline of krill and the increase and range expansion of salps, will alter export of organic matter and thus need to be incorporated into biogeochemical models that predict carbon sequestration.