Abundance and stable isotope composition of large and small mesozooplankton were analyzed in samples taken with 333 and 100 μm nets, respectively, at four sites in the eastern Mediterranean down to 4200 m depth in October 2001. Large mesozooplankton (333 μm nets) was sieved into five size fractions, and the δ13C and δ15N values of the fractions were measured as well as the δ15N values of total small mesozooplankton (100 μm nets) and specific mesozooplankton taxa. These measurements allow insights into the source of the diet and the trophic level relative to sinking and suspended particulate organic matter. Overall, biomass and abundance of zooplankton was low, reflecting the oligotrophic character of the eastern Mediterranean. Stable nitrogen isotope values of mesozooplankton were low (1–4‰) and close to zero in suspended particles at the surface. This indicates that the fixation of atmospheric nitrogen probably contributes to the N-pool in the eastern Mediterranean. Such low values were also found in sinking particles in deep waters and in most zooplankton size classes. However, suspended particles and mesozooplankton in the size class 0.5–1 mm, which was primarily composed of the deep-sea species Lucicutia longiserrata, showed higher values at depths below 1000 m. There is some indication that L. longiserrata was able to utilize the suspended particle pool in the deep eastern Mediterranean.