The study focuses on the question, how a seamount in the oligotrophic eastern Mediterranean affects the zooplankton community, as compared to the open water. Zooplankton samples were taken with 333 µm nets at two sites, the Rhodes Basin and the Anaximenes Mountain, in December 2006. The samples were sieved into size fractions, and the composition, biomass, abundance and stable isotope signatures were analysed. In general, biomass and abundance of zooplankton were low, reflecting the oligotrophic character of the eastern Mediterranean, but zooplankton standing stocks were higher at the Rhodes Basin than at the Anaximenes Mountain. Stable isotope signatures showed, at a generally low level, enrichment in zooplankton taxa along the food chain within the different pelagic zones and from the surface to the deep-sea, but no significant differences between Rhodes Basin and the seamount were evident in the food web structure. The zooplankton community in the Anaximenes Mountain region in the northern Levantine Basin seems not to be influenced by a local seamount effect, despite the difference in standing stocks between the seamount and the Rhodes Basin. This seems to be driven by larger-scale upwelling and downwelling structures of cyclones and anticyclones, dominating the circulation in the area.