Zooplankton species, which link primary production and higher trophic levels and play a major role in pelagic marine ecosystems, are associated with distinct water masses. In Fram Strait, the only deep-water connection between the Atlantic and Arctic Ocean, relatively warm Atlantic water (AW) enters the Arctic with the West Spitsbergen Current, whereas the East Greenland Current carries cold polar water masses southwards. Rising water temperatures might change the zooplankton community, with possible consequences for the food web. We therefore investigated the mesozooplankton abundance and community composition during two cruises with RV ‘Polarstern’ in summer 2011 (warm AW) and 2012 (cold AW). Vertical multinet hauls covering five different depth strata were taken along a transect at 78° 50’ N. In both years, the zooplankton abundance was higher in the eastern (AW) as compared to the western Fram Strait (Polar water), with copepods dominating the communities. The basic community composition did not change significantly between years at distinct sampling stations, despite temperature differences of ~2°C in AW. Thus, trends for future community changes might only be observable in the long term.