Variations in mesozooplankton diversity, community structure, and species assemblage related to environmental variability have been discussed regarding the Sea of Marmara, with particular attention to regulation by the holozoic dinoflagellate Noctiluca scintillans. Temperature stands alone as the most important factor affecting species succession and community structure while Noctiluca significantly influences zooplankton abundance and diversity, and appears as the prevailing factor for non-temperature dependent patterns in the zooplankton community. Competition between Marmara zooplankton and Noctiluca for the same food resources could be an important factor, considering the high production of the species when compared to herbivorous and omnivorous zooplankters. Meanwhile, chlorophyll a recorded throughout the study period indicated a sufficient food supply that could promote continuous mesozooplankton production in the region. Therefore top-down regulation of the zooplankton community by Noctiluca may gain importance. Noctiluca differed from other r-strategists mainly by its high competitive ability, year round occurrence, and large cell size. Therefore, zooplankton could not compete with Noctiluca in the long-term and Noctiluca found an opportunity to increase its abundance before the settlement of distinct summer or winter communities. Enhanced abundance, year-round occurrence, and high condition of Noctiluca population indicated that optimum conditions had been achieved for explosive development of the species in the Sea of Marmara. Increasing dominance of Noctiluca in the Sea of Marmara points out that the species could have a stronger affect on zooplankton in the following years and interrupt trophic pathways by reducing fodder zooplankton biomass. (c) 2005 Published by Elsevier Ltd.