Pteropods are an important component of the zooplankton community and hence of the food web in the Fram Strait. They have a calcareous (aragonite) shell and are thus sensitive in particular to the effects of the increasing CO2 concentration in the atmosphere and the associated changes of pH and temperature in the ocean. In the eastern Fram Strait, two species of thecosome pteropods occur, the cold water-adapted Limacina helicina and the subarctic boreal species Limacina retroversa. Both species were regularly observed in year-round moored sediment traps at ~ 200–300 m depth in the deep-sea long-term observatory HAUSGARTEN (79°N, 4°E). The flux of all pteropods found in the trap samples varied from < 20 to ~ 870 specimen m− 2 d− 1 in the years 2000–2009, being lower during the period 2000–2006. At the beginning of the time series, pteropods were dominated by the cold-water-adapted L. helicina, whereas the subarctic boreal L. retroversa was only occasionally found in large quantities (> 50 m− 2 d− 1). This picture completely changed after 2005/6 when L. retroversa became dominant and total pteropod numbers in the trap samples increased significantly. Concomitant to this shift in species composition, a warming event occurred in 2005/6 and persisted until the end of the study in 2009, despite a slight cooling in the upper water layer after 2007/8. Sedimentation of pteropods showed a strong seasonality, with elevated fluxes of L. helicina from August to November. Numbers of L. retroversa usually increased later, during September/October, with a maximum at the end of the season during December/January. In terms of carbonate export, aragonite shells of pteropods contributed with 11–77% to the annual total CaCO3 flux in Fram Strait. The highest share was found in the period 2007 to 2009, predominantly during sedimentation events at the end of the year. Results obtained by sediment traps occasionally installed on a benthic lander revealed that pteropods also arrive at the seafloor (~ 2550 m) almost simultaneous with their occurrence in the shallower traps. This indicates a rapid downward transport of calcareous shells, which provides food particles for the deep-sea benthos during winter when other production in the upper water column is shut down. The results of our study highlight the great importance of pteropods for the biological carbon pump as well as for the carbonate system in Fram Strait at present, and indicate modifications within the zooplankton community. The results further emphasize the importance of long-term investigation to disclose such changes.