We analyzed and compared Mediterranean mesozooplankton time series spanning 1957-2006 from six coastal stations in the Balearic, Ligurian, Tyrrhenian, North and Middle Adriatic and Aegean Sea. Our analysis focused on fluctuations of major zooplankton taxonomic groups and their relation with environmental and climatic variability. Average seasonal cycles and interannual trends were derived. Stations spanned a large range of trophic status from oligotrophic to moderately eutrophic. Intra-station analyses showed (1) coherent multi-taxa trends off Villefranche sur mer that diverge from the previous results found at species level, (2) in Baleares, covariation of zooplankton and water masses as a consequence of the boundary hydrographic regime in the middle Western Mediterranean, (3) decrease in trophic status and abundance of some taxonomic groups off Naples, and (4) off Athens, an increase of zooplankton abundance and decrease in chlorophyll possibly caused by reduction of anthropogenic nutrient input, increase of microbial components, and more efficient grazing control on phytoplankton. (5) At basin scale, the analysis of temperature revealed significant positive correlations between Villefranche, Trieste and Naples for annual and/or winter average, and synchronous abrupt cooling and warming events centered in 1987 at the same three sites. After correction for multiple comparisons, we found no significant correlations between climate indices and local temperature or zooplankton abundance, nor between stations for zooplankton abundance, therefore we suggest that for these coastal stations local drivers (climatic, anthropogenic) are dominant and that the link between local and larger scale of climate should be investigated further if we are to understand zooplankton fluctuations.