These data were used in a study on the impacts of mesozooplankton diversity on the functioning of pelagic ecosystems in the Sargasso Sea, at the Bermuda Atlantic Times-series Study (BATS). There were analyzed, together with semi-quantitative morphological data from individual mesozooplankton images to study variations of taxonomic and functional diversity, and the potential impacts of these variations on the carbon export in the ecosystem. This global dataset was also used to investigate the potential quantitative property of metabarcoding. Knowing more about mesozooplankton diversity and its impact on ecosystem functioning would allow to better represent it in biogeochemical models.