Mesozooplankton was sampled during one year in the eutrophicated Vranjic Basin and the influence of environmental variables on its abundance and distribution was analysed. Parallel microzooplankton samples were collected in order to assess trophic relationships within the zooplankton community. Total mesozooplankton abundances were high, exceeding 2×104 ind m−3 in the warmer part of the year, but the biodiversity was low. The annual variability of this assemblage was mostly influenced by temperature. Copepods were dominant among net plankton groups, while ciliates dominated the protozoan community. The key species of the copepod community were Acartia clausi, Oithona nana and Euterpina acutifrons, occurring simultaneously throughout the year. High abundances of small copepod Oithona nana were determined in both meso- and microzooplankton samples, and comparisons of the catches from 125 μm net and 5-l Niskin bottles revealed no significant differences between them. Significant correlation determined between Acartia clausi and oligotrich ciliates indicates predator–prey relationship and the importance of the ciliate community in the energy transfer through the trophic web of this area.