This dataset contains zooplankton community data collected at the Long-Term Ecological Research (LTER) station MareChiara, located in the Gulf of Naples, Mediterranean Sea (40.81°N, 14.25°E), operated by the Stazione Zoologica Anton Dohrn (SZN). Samples were collected through vertical net tows from 50 m depth to the surface using an Indian Ocean net (pre-2016) and a WP2 plankton net (from 2016 onwards). Zooplankton abundance is expressed as individuals per cubic metre. The dataset covers the period 1984–2024 and includes taxonomic identifications with WoRMS LSIDs, life-stage and sex annotations, and sampling instrument metadata following BODC NERC Vocabulary Server standards. Data are structured according to the Darwin Core Event core with Occurrence and Extended Measurement or Fact (eMoF) extensions, following OBIS data standards.