During 2005-2008 species composition, abundance patterns, natural mortality rates and salinity effects on zooplankton were studied in the Bosphorus regions of the Black and Marmara Seas. The tendencies to diminish for abundance and biomass of the Black Sea originated zooplankton species and to increase for the proportion of their carcasses in the direction from the Black Sea toward the Marmara Sea were found. The mortality in the Black Sea species increased with depth in the Marmara Sea. The contribution of organic matter of carcasses of the Black Sea originated organisms to bacterial processes in the deep strata of the Marmara Sea was estimated. Different salinity and temperature regimes restrict mutual penetration of the species in these seas. (C) 2010 Elsevier B.V. All rights reserved.