The dynamics of abundance and biomass of Noctiluca scintillans (Dinoflagellata) and Acartia clausi (Copepoda) in the Bosphorus area of the Black and Marmara Seas during 2005-2009 has been analyzed. Despite the fact that the more abundant Black Sea zooplankton community permanently enters the Marmara Sea, A. clausi and N. scintillans have formed independent populations in the northeast of the Marmara Sea. This may be confirmed on the one hand by the positive correlations between the numbers of A. clausi and N. scintillans individuals in the Marmara Sea near the Bosphorus Strait and near the Prince Islands and, on the other hand, by a lack of correlation between the abundance of these species in the Marmara Sea and in the Bosphorus area of the Black Sea. The abundance of N. scintillans was 6-10 times lower in the Black Sea near the Bosphorus Strait than that in the Marmara Sea. A high correlation (r = 0.84) between the abundance of N. scintillans and the number of dead A. clausi females near the Bosphorus Strait in the Marmara Sea suggests an important role of necrozooplankton in the development of the dinoflagellate.