Zooplankton plays a central role in marine trophic webs, where community indexes (diversity, abundance, and biomass) are affected by regional and local oceanographic conditions. The multinational conservation initiative, known as the Eastern Tropical Marine Corridor (CMAR) encompasses a network of Marine Protected Areas of unique and high biological diversity along the Eastern Tropical Pacific. Zooplankton studies in this area are scarce and recently conducted. In the northern zone of Coiba Island (Coiba National Park, Panamá) during the dry and rainy seasons (2019–2020), the composition, abundance, and biomass of mesozooplankton and its relationship with oceanographic variables (temperature, salinity and euphotic zone) were analyzed. In both seasons different oceanographic conditions were found with vertical heterogeneities of temperature (T) and salinity and seasonal significant differences in minimum of T and euphotic zone depth (EZ). Zooplankton abundance and total biomass showed positive associations, and maximum values during the dry season; in oblique trawls, total zooplankton biomass showed negative associations with T (−0,60) and positive with Secchi disk depth (0.67). These patterns suggest higher zooplankton productivity during dry season associated with oceanographic conditions in the North zone of Coiba Island. Organisms were classified to the lowest taxonomic level possible (Sub-family or Genus) and a total of 33 zooplankton taxa were identified. In the holoplankton the most important groups were Copepoda, Chaetognata, Appendicularia and Thaliacea, while in the meroplankton larvae of Crustacea, Echinodermatha and Mollusca were the most common groups. Zooplankton indexes (abundance, biomass and composition) were similar to those reported for other CMAR islands. Strategies recommended to strengthen biodiversity conservation in this MPA include more studies on taxonomy, trophic dynamics, and connectivity of planktonic communities as central link in marine trophic webs.