Mesozooplankton group composition was examined in the Northeastern Aegean Sea (NEA) over a grid of 30 stations sampled during July 2004. The surface water layer influenced by the low salinity Black Sea waters (BSW) is considered in this paper. We attempted to study horizontal distribution patterns of major mesozooplankters within a more comprehensive framework, taking into account not only hydrology but also available, concurrently collected data on lower trophic levels (autotrophic and microbial heterotrophic communities). BSW was mainly restricted in the eastern part of the surveyed area where it was entrapped in a ca. 50-km wide anticyclone (the "Samothraki" gyre). High Chlα concentrations, autotrophic biomass as well as abundance and biomass of mesozooplankton were associated with the BSW, with the highest values recorded inside the gyre as well as at its coastal northern periphery and the lowest values towards the western and offshore part of the surveyed area characterized by high salinity waters of Levantine origin. Among mesozooplankters, cladocerans (mainly Penilia avirostris) showed a high abundance within the gyre in contrast to the very low abundance of copepods and appendicularians. Low salinity-high temperature gyre waters were characterized by the dominance of cyanobacteria of the genus Synechococcus in autotrophic biomass and the significant contribution of heterotrophic nanoflagellates in microbial heterotrophic biomass. Based on existing knowledge on ecophysiological traits and prey size-spectra selectivity, we discuss the observed distribution patterns of major mesozooplankton groups in terms of ambient abiotic parameters and the possible biological interactions among these groups as well as with lower or upper trophic levels.