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Temporal changes in mesozooplankton abundance affect planktonic food web interactions and biogeochemistry. We enumerated mesozooplankton from monthly day and night tows in the epipelagic zone at the Bermuda Atlantic Time-series Study (BATS) site in the Sargasso Sea (1999-2010). Abundances of each taxon were determined using a ZooScan imaging system and microscopy. Generalized linear models were used to determine environmental parameters that best explained abundance patterns. Taxa with pronounced diel vertical migration included euphausiids, amphipods, Limacina spp. pteropods, and other shelled pteropods. Taxa with a pronounced spring abundance peak included euphausiids, appendicularians, and Limacina spp., while harpacticoid copepods peaked in late summer, and calanoid copepods in late winter/early spring and summer. Many taxa increased in 2003, coincident with a diatom bloom and the largest primary production peak in the time series. Long-term, increasing trends occurred in calanoid and oncaeid copepods, and ostracods, with barnacle nauplii significantly increasing. Sub-decadal-scale climate oscillations and long-term warming may be driving decreases in shelled pteropods and appendicularians. Chaetognath abundance increased in response to increased density of a major prey taxon, calanoid copepods. Calanoid copepods and ostracods increased with increasing water column stratification index and the Atlantic Multidecadal Oscillation index, indicating warmer sea surface temperatures favour these taxa.