Abstract Coordinated cruises conducted in the Black Sea offshore waters in spring and autumn 2008, within the framework of European project SESAME, allowed to obtain a quasi-synoptic picture of the mesozooplankton standing stock and community composition. A clear spatial difference in total abundance was observed in spring with higher values over the slope than over the deep basin, due to the development of the fast boundary current. In autumn, standing stock was lower than in spring; weakening of the boundary current and extensive eddy formation caused small-scale variability in mesozooplankton distribution and intensification of the exchange between the different parts of the sea. In both seasons, copepods comprised the bulk (62-95%) of mesozooplankton biomass. Community composition variability was tested for the first time using data obtained from the entire basin; the application of neural network analysis (Self-Organizing Maps) revealed a rather homogenous picture of community composition. The development of cladocerans in autumn resulted in the differentiation of the slope areas from the deep basin. Mass development of the heterotrophic dinoflagellate Noctiluca scintillans was observed in the western and north-western areas in autumn. No change in standing stock values and community composition seem to have occurred since 2000 in the north-eastern region.