In the open ocean, seamounts hold high ecological relevance for local communities. Zooplankton aggregations are often observed above these topographic features, supporting the spawning and foraging of a wide diversity of species. This study provides novel insights into the zooplankton communities inhabiting the Madeira-Tore seamount complex, located in the northeastern Atlantic Ocean. The findings contribute valuable information to ongoing efforts in biodiversity assessment and marine conservation planning. Zooplankton samples were collected from the neustonic layer of the Madeira-Tore region using a Manta trawl net, during an oceanographic research survey conducted in 2022. The organisms were morphologically identified, and taxonomic analyses revealed highly diverse communities, including copepods, gelatinous zooplankton, decapod larvae, amphipods, polychaetes, and fish larvae. Notably, several species rarely observed in coastal areas, and some newly recorded for the region, were documented, highlighting the uniqueness and ecological value of these offshore habitats. In selected cases, integrative taxonomy was applied, combining morphological observations with molecular tools to confirm the species identity and resolve taxonomic uncertainties. The findings emphasized the ecological significance of the Madeira-Tore complex and added important data to understand the dynamic and understudied ocean–atmosphere interface. This study underscores the need to integrate zooplankton data into marine spatial planning and the designation of Marine Protected Areas, while also contributing to a broader understanding of trophic dynamics and biogeochemical cycling in open-ocean ecosystems.