The vertical distributions of the unicellular cyanobacteria Synechococcus were studied in several highly contrasting seas: the Black Sea, Sea of Marmara, Aegean Sea, and Mediterranean Sea. Cell abundances varied significantly on both vertical and horizontal scales in all physically and spatially discrete water masses. Epifluorescence microscope cell counts from all seas clearly showed that majority of the population remains suspended in the surface-mixed layer and decreases gradually towards the base of the euphotic zone. Surface spatial distributions in the Black Sea were heterogeneous. Salinity, rather than temperature, seemed to have the greatest impact on the surface distribution of cells in this highly eutrophic sea. Changes in abundance in the mixed layer were small compared to the abrupt changes below the halocline, especially in the Black Sea and the Sea of Marmara. In contrast to the Black Sea, the major population remains suspended above the depth of fluorescence maximum in the Aegean and eastern Mediterranean seas. Significant correlations (r > P(0.01)) were observed between cell counts and physical and chemical parameters with depth in the Black Sea. In all seas, cells at subsurface chlorophyll-a maximum layer (SCML) reflected brighter and longer fluorescence than those present at the surface and below. Cell size derived from flow cytometry indicated the presence of larger cells at the surface mixed layer compared to those at depth. (c) 2006 Elsevier Ltd. All rights reserved.