Zooplankton communities vary in space and time. Their composition is strongly influenced by lower trophic levels that are dependent on the availability of light and nutrients. As all marine ecosystems are relying on zooplankton as intermediate trophic step between primary production and higher trophic levels, changes in the zooplankton community composition and biomass can cascade through the food web with important impacts on fish communities and through that on fisheries yields. An intense fisheries exist around the Falkland Islands in the SW Atlantic Ocean, around 51° S, but to the best of our knowledge, no previous study has to date investigated the seasonal variation in zooplankton community composition in these waters. We show that copepods (39.2%), the larvae of the anomurid Grimothea gregaria (33.1%) and euphausiids (10.9%) dominate the local mesozooplankton community by biomass. All species showed seasonal patterns, including ontogenetic behaviour of G. gregaria migrating to deeper waters with development, which were significantly explained by temperature (p < 0.001). While overall biomass significantly decreased with distance from shore (p < 0.001), mesozooplankton diversity was highest at 30 km from shore. The presented study is the first assessment of the mesozooplankton biomass off the Falkland Islands and provides a first baseline to aid future ecosystem studies in the context of ecosystem based fisheries management in the region.