Mesozooplankton samples were collected during October-November 1991 in the Eastern Mediterranean Sea from four discrete depth layers in the upper 300 m water column and were analysed at copepod species level. Differentiation of species composition with depth was clear, suggesting the existence of an epipelagic (0-100 m) and a mesopelagic (100-300 m) community. Correspondence analysis revealed similarities among areas for the 0-50 m layer, due to the dominance of Clausocalanus furcatus and Oithona plumifera. Dissimilarities among areas appeared below 50 m and increased with depth, discriminating between different copepod assemblages. These dissimilarities appear to be related to different hydrological features (cyclonic gyres or anticyclonic gyres) prevailing in the basin, rather than to the geographical position of stations and/or to water masses distribution.