The Mediterranean and the Black Seas are connected through Bosphorus, Marmara Sea and Dardanelles (Turkish Straits System, TSS). In this study, we examined the spatial distribution of copepods and investigate their production and grazing. The aim was to understand the transfer of phytoplankton/microzooplankton production up the food chain in TSS and Aegean Sea during spring. The phytoplankton and microzooplankton biomass and production showed a clear decreasing trend from Bosphorus to the Aegean Sea, whereas copepod biomass did not reveal any distinct trend and only the number of copepod species increased from Bosphorus to the Aegean Sea. Production of copepods and egg production showed similar trends except for the Bosphorus, where production of copepods was very low due to the low copepod biomass in this area. In all areas, the copepod carbon demand was largely met by phytoplankton and microzooplankton production. However, only a low amount of primary production was consumed by copepods and production appeared to flow mostly through other pathways (microbial loop) and/or sediment on the bottom. The results of this study confirm the hypothesis that there is a substantial differentiation within pelagic food web structure and carbon flow from Bosphorus to the Aegean Sea. (C) 2011 Elsevier B.V. All rights reserved.