Shelled (thecosome) and naked (gymnosome) pteropods are regular, at times abundant, members of Southern Ocean zooplankton assemblages. Regionally, shelled species can play a major role in food webs and carbon cycling. Because of their aragonite shells thecosome pteropods may be vulnerable to the impacts of ocean acidification; without shells they cannot survive and their demise would have major implications for food webs and carbon cycling in the Southern Ocean. Additionally, pteropod species in the southwest Atlantic sector of the Southern Ocean inhabit a region of rapid warming and climate change, the impacts of which are predicted to be observed as poleward distribution shifts. Here we provide baseline information on intraseasonal, interannual and longer scale variability of pteropod populations off the Antarctic Peninsula between 1994 and 2009. Concentrations of the 4 dominant taxa, Limacina helicina antarctica f. antarctica, Clio pyramidata f. sulcata, Spongiobranchaea australis and Clione limacina antarctica, are similar to those monitored during the 1928–1935 Discovery Investigations and reflect generally low values but with episodic interannual abundance peaks that, except for C. pyr. sulcata, are related to basin-scale climate forcing associated with the El Niño-Southern Oscillation (ENSO) climate mode. Significant abundance increases of L. helicina and S. australis after 1998 were associated with a climate regime shift that initiated a period dominated by cool La Niña conditions and increased nearshore influence of the Antarctic Circumpolar Current (ACC). This background information is essential to assess potential future changes in pteropod species distribution and abundance associated with ocean warming and acidification.